Over-Production of Secondary Metabolites by Over-Expression of the VEA Gene

ABSTRACT

The invention provides a general and facile method to obtain secondary metabolites from fungal sources. The invention is based on the discovery that the fungal gene veA and protein encoded thereby regulates the activity of multiple secondary metabolite gene clusters in fungi. Over expression of the gene veA provides increased production of secondary metabolites in engineered cells. In particular, such a method of increasing secondary metabolite production allows the production of improved yields of valuable secondary metabolite products.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. 12/799,505, filed Apr. 26, 2010, which claims priority to U.S. Provisional Application No. 61/172,514, filed Apr. 24, 2009, both of which are incorporated by reference for all purposes.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under 0236393 awarded by the National Science Foundation and 09-CRHF-0-6055 awarded by the USDA/CSREES. The government has certain rights in the invention.

FIELD OF THE INVENTION

The invention relates generally to methods of over-producing secondary metabolites. More particularly, the present invention is directed to methods of over-producing secondary metabolites by manipulating fungal regulatory genes involved in the control of secondary metabolite gene clusters.

BACKGROUND OF THE INVENTION

Secondary metabolites are organic compounds that are not directly involved in the normal growth, development or reproduction of organisms. They are often used as defenses against predators, parasites and diseases, for interspecies competition, and to facilitate the reproductive processes (coloring agents, attractive smells, etc).

Secondary metabolites of fungi include both “friends and foes” of human health. For example, penicillin and derivatives produced by Aspergillus, Cephalosporium and Penicillium species are widely used antibiotics, lovastatin is a potent cholesterol-lowering drug produced by Aspergillus terreus and aflatoxins, produced by several Aspergillus species, are highly toxic carcinogens contaminating many crops.

Secondary metabolic pathways are often tightly correlated with the fungal developmental program and response to external cues including light. Since secondary metabolites are usually restricted to a much more limited group of organisms, they have long been of prime importance in taxonomic research. Secondary metabolites are especially useful for drug or other technological development, or as an inspiration for unnatural products. Biosynthetic genes for fungal secondary metabolites are often clustered and regulated by pathway-specific transcription factors. Secondary metabolism is also regulated at an upper hierarchic level by a global epigenetic control mechanism. However, methods of producing large amounts of secondary metabolites are difficult and provide unpredictable results. Therefore a need exists for methods of producing large amounts of secondary metabolites that address these problems.

The distribution of natural products is characteristically restricted to certain fungal taxa, particularly the Ascomycetes. Perhaps the greatest number of known secondary metabolites has been ascribed to the Ascomycete genus Emericella (asexual stage=Aspergillus). Much of the current understanding of fungal secondary metabolite regulation arises from studies of the genetic model Aspergillus nidulans. This organism produces many natural products including sterigmatocystin ST (ST; the penultimate precursor to aflatoxin) and penicillin and has been used as a heterologous host to study the biosynthesis of other natural products including lovastatin. Critical advances in understanding fungal secondary metabolism have been largely based on primary studies from A. nidulans and/or secondary studies in other fungi where researchers were able to exploit the knowledge gained from A. nidulans to their fungus of choice.

A. nidulans, a mold, produces many compounds relevant to biotechnology and human health and is a well-suited model for the analysis of the interplay between secondary metabolism, light and differentiation. A. nidulans grows vegetatively in the soil by hyphal tip extension until competent for development and secondary metabolism. In reproduction, A. nidulans forms airborne asexual spores in light but preferentially undergoes sexual reproduction in the dark. Sexual reproduction in the dark results in an increase in secondary metabolism and in the formation of sexual fruit bodies called cleistothecia, which consist of different cell types. Mutations resulting in defects in fungal development often impair secondary metabolism. There is genetic evidence for a connection between fruitbody formation, secondary metabolism, and light in A. nidulans reproduction, but the molecular mechanism is not known.

Aspergillus flavus, an opportunistic pathogen of oil seeds, occurs as a saprophyte in soils worldwide and colonizes several important agricultural crops, such as maize, peanut, and cottonseed, before and after harvest. The pathogen generates asexual spores, conidia, as the source of inoculum and overwinters as sclerotia which germinate to produce conidia in the subsequent season. A. flavus and other aspergilli, such as Aspergillus parasiticus, can produce the polyketide-derived carcinogenic secondary metabolite aflatoxin. In the United States, annual yield losses in the million-dollar range from aflatoxin contamination on peanut and maize crops are frequently reported. Aflatoxin-contaminated food and feed is also a major problem in developing countries, especially in Asia and Africa. Recently, an outbreak of aflatoxin poisoning from maize was reported to have killed a hundred people in Kenya. Therefore, measures to control Aspergillus infections and aflatoxin production are urgently needed to protect human and animal health. The identification and characterization of molecules necessary for A. flavus conidial, sclerotial, and aflatoxin production are critical to develop rational control strategies.

VeA, a conserved velvet protein encoded by the veA gene, increases expression during sexual development. However, VeA transport into the nucleus is inhibited by light. It acts as a negative regulator of asexual development. VeA is required for cleistothecial production in A. nidulans and sclerotial production in both A. parasiticus and A. flavus. In addition, the VeA gene regulates the expression of sterigmatocystin (a precursor of aflatoxin) and penicillin genes in A. nidulans and aflatoxin genes in A. parasiticus and A. flavus. VeA interacts with LaeA in an as-yet-unclear mechanism, althouth analysis shows that VeA and LaeA negatively regulate each other at the transcript level in A. nidulans (1) and LaeA negatively regulates veA in A. flavus (21).

LaeA, another protein located in the cell nucleus, is present in numerous fungi and is a master regulator of secondary metabolism in Aspergilli and other fungal genera. LaeA is also necessary for sclerotial formation in A. flavus and affects cleistothecial development in A. nidulans.

The deletion of LaeA silences numerous secondary metabolite gene clusters, including those responsible for the syntheses of the antibiotic penicillin as well as for toxins such as ST or gliotoxin. It has been suggested that LaeA might control the accessibility of binding factors to chromatin regions of secondary metabolite clusters because LaeA prevents heterochromatin maintenance of some clusters.

Other factors have been reported which link morphological development with secondary metabolism. Of particular interest are a family of oxylipin-producing oxygenases (encoded by ppo and lox genes) which have been shown to balance ascospore and conidial production in A. nidulans (40, 41) and sclerotial and conidial production in A. flavus, as well as secondary metabolite production in both species. Most recently, a density-dependent switch from sclerotial-to-conidial development in A. flavus was found to be affected by oxylipin production. Both oxylipin production and the response to oxylipin signaling are dependent on an intact VeA protein. VeA is also required for ppoA expression, and VeAPpoA interactions affect both sexual and asexual development in A. nidulans. The impact of the loss of these proteins on pathogenesis has been explored to some degree for LaeA and Ppo mutants but not yet reported for VeA. LaeA is a key determinant in aspergillosis caused by A. fumigatus and seed rot by A. flavus and Ppo loss impacts virulence attributes of A. fumigatus, A. nidulans, and A. flavus.

Despite present methodologies, a need exists for improved methods of controlling production of secondary metabolites to obtain improved production of important natural products and/or novel natural products with medicinal value.

BRIEF DESCRIPTION OF THE DRAWINGS

The present patent application contains at least one drawing executed in color. Copies of this patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1(A) shows identification of VeA-associated proteins in A. nidulans. Brilliant blue G-stained 10% SDS-polyacrylamide gel electrophoresis of TAP procedure for VeA. kD, kilodaltons. (B) The polypeptides identified from the bands of affinity purification belong to corresponding proteins (details in table 4). (C) Domain mapping of the interactions based on Y2H data (FIG. 4). N, N terminus; C, C terminus.

FIG. 2(A) shows Modified TAP tag* and VeA expression. Depiction of the TAP tag. The codons for 18 amino acids were changed by site-directed mutagenesis and are designated as differently colored spheres. (B) Immunoblotting with antibody against calmodulin binding peptide: 85 kDa VeA::TAP* tag. In the light (L), expression is relatively low in comparison to the expression in the dark (D); as a control antiactin antibody was used. (C) Brilliant Blue G-stained 10% SDS-PAGE gel of the TAP for VelB and LaeA. (D) The polypeptides identified from the bands of two affinity purifications belong to corresponding proteins (see Table 4).

FIG. 3(A) shows velB gene structure and alignment of VeA (SEQ ID NO: 116) and VelB (SEQ ID NO: 117; Genbank Accession No. CBF89638). Architecture of the velB locus of A. nidulans. Exons are indicated as E1, E2, E3, E4 (confirmed in cDNA) and recognition sites of common restriction endonucleases are shown. (B) Local alignment of the VelB and VeA proteins. Identical residues are indicated by an asterisk (*), conserved amino acid substitutions (similar amino acids) as two dots (:), and semi-conserved amino acid substitutions as one dot (.). The red rectangle indicates a putative nuclear localization signal (NLS) of VeA, the blue rectangle indicates a putative nuclear export signal (NES) and the black rectangle marks a conserved PEST (Pro, Glu (or Asp), Ser, Thr) motif. Red: small and hydrophobic (including aromatic amino acid), Blue: acidic, Magenta: basic, Green: hydroxyl, amine and basic amino acids. (C) Northern hybridization of VelB during different life stages of A. nidulans. It is highly expressed in asexual conidia and sexual ascospores. VelB expression stays at basal levels during vegetative growth and increases during late asexual (24, 48 h) or sexual (98 h and ascospores) development.

FIG. 4. Interaction domain mapping among VeA, VeA1, VosA, LaeA and VelB by yeast two-hybrid assay. Derivatives of yeast strain L40 expressing the different bait and prey fusion proteins were spotted in serial dilutions for growth on -UHTL (uracil, histidine, tryptophan and leucine), -UHTL with 5 mM 3-AT and -UTL media, and then incubated at 30° C. for 5 days. Their β-galactosidase activities were analyzed using ONPG.

FIG. 5(A) shows BiFC studies of velvet complex components and their effect on ST production. Enhanced yellow fluorescent protein fused to the N terminus of veA gene (N-EYFP::VeA) interacts with C-EYFP::LaeA in vivo, which is indicated as yellowish green specks in the nucleus. Histone 2A red fluorescent protein (H2A::mRFP) fusion visualizes the entire nucleus. Interaction does not take place in the whole nucleus but in certain points (gene clusters) that LaeA probably acts on (indicated by arrows). Differential interference contrast (DIC) shows hyphal cells. (B) N-EYFP::VeA fusion protein interacts with C-EYFP::VelB in the cytoplasm and nucleus. (C) ST production in respective mutant backgrounds and WT at different time points. STs, ST standard; V20, 20 hours vegetative growth; L, light; D, dark. 24 and 48 hour time points are shown. (D) Quantification of ST production using thin layer chromatography: In the dark, more ST is produced in the WT. Deletion of either laeA or veA results in no ST above background (denoted by B) fluctuations. Loss of velB results in basal ST production in dark.

FIG. 6(A) shows Deletion of velB and impairment of sexual fruit body formation. Phenotypic characterization of the velBΔ deletion strain AGB279. Defects are restored in AGB280 (+velB). Fruit body formation (FB) in TNO2A3 and AGB280 appeared as normal (red arrows), whereas aerial hyphae (white arrows) and red pigment accumulation accompanied by a lack of fruit bodies were evident for velBΔ and veAΔ strains. Pictures of cleistothecia and hyphae were taken at 10⁸-fold magnification. (B) ST standard HPLC (retention time (RT): 21.58) and the corresponding mass spectrum. (C) Confirmation of sterigmatocystin (ST) production by LC-MS in the velBΔ mutant. HPLC condition: A=0.1% formic acid in water, B=acetonitrile+0.1% formic acid, gradient=2% B to 100% B in 30 min, re-equil=18 min/flow rate=0.200 ml/min, column=ZORBAX C-18 SB, 2.1×50 mm (100 Å, 1.8 U Agilent), Temperature=40° C. Mass spectrum condition: Agilent ESITOF, source Temp=325° C., electrospray=3500 V, drying gas=91/min, nebulizer gas=30 PSI. Tolerance=less than 3 ppm. Actual was 1.6 ppm at Mass 325.0712.

FIG. 7. Expression of extra copy of laeA in the veAΔ background. RDIT9.32 (wild-type) and RJW108.1 (veAΔ::argB; trpC::laeA) were grown on sexual induction condition and metabolites extracted and run on a thin layer chromatography plate (chloroform:acetone=4:1). An extra copy of laeA does not restore sterigmatocystin in the veAΔ background. ST=sterigmatocystin standard.

FIG. 8. Northern blot analyses. Levels of veA, velB, laeA mRNA in WT. (RDIT9.32), laeAΔ (RJW41.A), veAΔ (RJW112.2) and velBΔ (RNI18.2). All strains were grown in liquid Aspergillus rich medium at 37° C., 250 rpm for 20 h (shown as V20 in the figure) and then transferred onto solid MM plus supplements with or without 0.1% casamino acids for the concomitant induction. The strains grown on MM without casamino acids were incubated at 37° C. under white fluorescent light (shown as L in the figure), while the strains grown on MM with casamino acids were sealed with parafilm, wrapped with foil and incubated at 37° C. in the darkness (shown as D in the figure). Samples for RNA extraction were collected at 24 h and 48 h after induction. Twenty micrograms of total RNA were loaded in each lane. EtBr-stained rRNA evaluated equal loading of total RNA.

FIG. 9(A) shows Subcellular localization of the subunits of the velvet complex. VeA-, LaeA-, and VelB-sGFP localizations in the presence or absence of light. VeA-sGFP shows light-dependent nuclear enrichment (counterstained with H2A::mRFP for visualization of the entire nucleus). (B) Nuclear/cytoplasmic GFP signal ratio of 100 hyphal cells each (Openlab software 5.0.1). Growth in the dark results in increased nuclear and decreased cytoplasmic fluorescence for VeA. VelB and LaeA distribution is hardly affected by illumination.

FIG. 10(A) shows VeA supports nuclear localization of VelB and formation of the velvet complex. Fluorescence patterns in strains expressing velB::sgfp in the dark in veA+ and veAD backgrounds. (B) Nuclear/cytoplasmic GFP signal ratio of 100 hyphal cells each. Nuclear signal intensity is higher in the veA+ strain background than in veAD. (C) Model: (Light) VeA is mostly retained in the cytoplasm, VelB supports asexual spore formation, and LaeA shows low activity. (Dark) An increased amount of VeA is imported into the nucleus by KapA and, in addition, supports the nuclear transport of VelB. Dotted lines indicate the decreased amount of VeA that is present in the cell in the light and the impairment of VeA nuclear transport in the light. VelB/VeA control development and LaeA activity by formation of the velvet complex that affects secondary metabolite clusters expression.

FIG. 11(A) shows Deletion of the velB locus and TAP tagging fusion genes at the velB and laeA loci. Comparative depiction of the wild-type velB locus (TNO2A3) and the velB::ptrA locus (AGB279). The black bar indicates the probe for Southern hybridization. (B) The result of TAP tagging of velB locus is depicted. Autoradiography of Southern hybridization confirms the gene replacement. (C) The TAP tagged laeA locus is shown. Autoradiography of Southern hybridization confirms the homologous gene replacements for the velB and laeA loci. For the deletion of velB, the ptrA (pyrithiamine resistance gene) marker was used and for the TAP tagging of velB and laeA, the (nourseothricin resistance gene) nat marker was utilized.

FIG. 12. Sequence Listing for VeA (A. nidulans) (SEQ ID NO: 116).

FIG. 13(A) shows Deletion, MCveA, and MClaeA mutants of A. flavus. Diagram of the strategy of replacement of A. flavus NRRL 3357.5 veA with A. fumigatus AF293 wild-type pyrG gene shows the restriction enzyme digestion sites of KpnI for Southern analysis with veA probe. To confirm gene replacement or MC transformants using Southern analysis, at least two restriction enzymes for each probe were utilized, KpnI (K) and SapI (data not shown) for veA and HindIII (H) and BamHI (data not shown) for laeA. A. fumi, A. fumigatus. (B) Southern analysis. The KpnI digest shows 6.8-kb and 1.1-kb veA fragments in the wild type and 4.7-kb, 2.2-kb, and 1.1-kb fragments in the AveA strain. The MCveA strain shows both wild-type 6.8-kb and 1.1-kb fragments, as well as 3.6-kb and 0.3-kb (not shown) fragments. The laeA probe presented a 5.6-kb fragment in the wild type; 4.5-kb, 3.2-kb, and 1.7-kb fragments in the ΔlaeA strain; and several extra bands in the MClaeA strain. The laeA mutants have been described before, in reference 21. WT, wild type.

FIG. 14. Colony diameters of veA and laeA mutants of A. flavus. A 5-μl amount of a suspension of 10⁶ spores/ml of each strain was point inoculated on 30 ml of 1.6% GMM. Cultures were grown at 29° C. under continuous dark or light conditions, and growth diameters measured at 3 and 6 days after inoculation. Letters indicate differences between strains that were statistically significant (P<0.05) according to the Tukey-Kramer multiple comparison test. Error bars show the standard deviations of the results of four replications. Strains were grown in both light and dark conditions. WT, wild type.

FIG. 15. Gene expression levels of veA and laeA in A. flavus mutants. Each strain was grown in liquid GMM culture with shaking (250 rpm at 29° C.) under dark conditions. Total RNA was extracted from two replicates at 48 hrs after inoculation. Northern blots were probed with internal or ORF fragments of each gene (Table 2). rRNA and actin were the loading and expression controls. WT, wild type.

FIG. 16(A) shows Effects of veA and laeA allele numbers on density-dependent conidial and sclerotial production in A. flavus. Each strain was grown from 10², 10⁴, and 10⁶ spores/plate as described in Materials and Methods. Conidial counts. (B) Sclerotial weight. Letters indicate statistically significant differences (P<0.05) for each strain at different population levels according to the Tukey-Kramer multiple comparison test. Error bars show standard deviations of the results of four replications. WT, wild type.

FIG. 17. Aflatoxin production of veA and laeA mutants. Aflatoxin from each strain was assessed at three different spore inoculation levels. The experiment was replicated three times, as shown. C, aflatoxin B1 control; WT, wild type.

FIG. 18(A) Conidium production and aflatoxin production on peanut and maize seeds. Seeds of two peanut cultivars and one maize line were inoculated with 10⁵ spores/ml of the wild type and the veA and laeA mutants and incubated for either 3 days (peanut cultivar SunRunnner and maize kernels) or 5 days (peanut cultivar FloRunner) after inoculation at 29° C. under dark conditions. For conidium counting, 1-ml amounts of homogenized suspensions of five peanut cotyledons or maize kernels of inoculated seeds were diluted to 1× and conidia counted. Letters indicate statistically significant differences (P<0.05) of different strains, according to Tukey-Kramer multiple comparison test. Error bars show the standard deviations of the results of three replications. (B) Aflatoxin was extracted from inoculated peanut cotyledons and maize kernels and resuspended in 500 μl of chloroform, and 10 μl of each extract was spotted on a TLC plate and separated with chloroform/acetone (95:5, vol/vol). C, aflatoxin B1 control; WT, wild type; MOCK, control inoculated with water.

FIG. 19(A) Histological examination reveals differences in seed ingress and lipid utilization of ΔveA and ΔlaeA strains compared to these functions in the wild type. Tissues were stained with Gomori methenamine-silver for detection of fungal hyphae. (B) Tissues were stained with Nile red for lipid body detection in seeds. To observe tissues, a bright-field microscope was used for Gomori stain and a tetramethyl rhodamine 5-isothiocyanate filter in a fluorescent microscope was used for Nile red. Seeds infected with the wild-type fungus show diminishment of lipid bodies near the surface (white line) of the seed. Scale bars=100 μm. WT, wild type; Mock, control inoculated with water.

FIG. 20. Loss of veA and laeA sensitizes the fungus to oleic acid. Inhibition of colony diameters of ΔveA and ΔlaeA mutants but not the wild type is observed when GMM is supplemented with 6 mM oleic acid at 3 (data not shown) and 6 days after inoculation. Letters indicate statistically significant differences (P<0.05) at 6 days after inoculation with different strains, according to Tukey-Kramer multiple comparison test. Error bars show the standard deviations of the results of four replications. WT, wild type; g, glucose; hexanoic, hexanoic acid; oleic, oleic acid; erucic, erucic acid.

SUMMARY OF THE INVENTION

The present invention provides a novel method of increasing the amount of a secondary metabolite produced by a cell or organism. The method comprises the steps of obtaining a cell or an organism capable of biosynthesizing a secondary metabolite; transforming the cell or organism with a nucleic acid which encodes a veA polypeptide, a polypeptide having substantial sequence identity thereto, or a fragment thereof having secondary metabolite gene cluster regulating activity; and culturing the transformed cell or organism so that an increase in production of the secondary metabolite occurs in the transformed cell or organism as compared to a non-transformed cell or organism. In one embodiment, the cell or organism is an Aspergillus species such as A. nidulans or A. flavus.

In another embodiment, the present invention provides a novel method of decreasing the production of a secondary metabolite by a transformed cell or organism. The method comprises the steps of: obtaining a transformed cell or organism capable of biosynthesizing a secondary metabolite, the transformed cell or organism having a defective veA gene wherein the defective veA gene is no longer biologically active and expression of secondary metabolite gene clusters is reduced; and culturing the transformed cell or organism so that a decrease in production of the secondary metabolite occurs in the transformed cell or organism as compared to a non-transformed cell or organism. In one embodiment, the cell or organism is an Aspergillus species such as A. nidulans or A. flavus.

In another embodiment, the present invention provides a novel method of producing an isolated secondary metabolite. The method comprises the steps of: obtaining a cell or an organism capable of biosynthesizing a secondary metabolite; transforming the cell or organism with a nucleic acid which encodes a veA polypeptide, a polypeptide having substantial sequence identity thereto, or a fragment thereof having secondary metabolite gene cluster regulating activity; culturing the transformed cell or organism under conditions conducive to increasing production of the secondary metabolite in the transformed cell or organism as compared to a non-transformed cell or organism; and recovering the secondary metabolite from the transformed cell or organism or from the culture in which the transformed cell or organism was grown in an isolated form. In one embodiment, the cell or organism is an Aspergillus species such as A. nidulans or A. flavus.

In another embodiment, the present invention provides a novel method for identifying a novel secondary metabolite biosynthesis gene cluster in a fungus. The method comprises the steps of: obtaining a transformed fungus having a disrupted veA gene; isolating a sample of nucleic acids from the transformed fungus, wherein the sample of nucleic acids is representative of the expressed genes of the transformed fungus; hybridizing the sample of nucleic acids isolated above or nucleic acid equivalents of same with an array comprising a plurality of nucleic acids representative of the expressed genes of a non-transformed fungus under conditions conducive to forming one or more hybridization complexes; detecting the hybridization complexes; comparing the detected levels of the hybridization complexes with the level of hybridization complexes detected in a sample of nucleic acids isolated from a veA-expressing fungus, wherein the nucleic acids isolated from a veA-expressing fungus are representative of the expressed genes of the veA-expressing fungus, and wherein an altered level of hybridization complexes detected above compared with a level of hybridization complexes of the sample of nucleic acids from the veA-expressing fungus correlates with and identifies at least one gene under regulatory control of a veA gene product; and examining genomic nucleotide sequence surrounding the at least one gene identified above to determine if the at least one gene is clustered with other secondary metabolite biosynthesis genes, thereby identifying a novel secondary metabolite biosynthesis gene cluster. In one embodiment, the cell or organism is an Aspergillus species such as A. nidulans or A. flavus.

DETAILED DESCRIPTION OF THE INVENTION I. IN GENERAL

Before the present materials and methods are described, it is understood that this invention is not limited to the particular methodology, protocols, materials, and reagents described, as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by any later-filed nonprovisional applications.

It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. As well, the terms “a” (or “an”), “one or more” and “at least one” can be used interchangeably herein. It is also to be noted that the terms “comprising”, “including”, and “having” can be used interchangeably.

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); Cell Culture and Somatic Cell Genetics of Plants, Vol. 1 (I. K. Vasil, ed. 1984); R. V. Stanier, J. L. Ingraham, M. L. Wheelis, and P. R. Painter, The Microbial World, (1986) 5th Ed. Prentice-Hall.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications and patents specifically mentioned herein are incorporated by reference for all purposes including describing and disclosing the chemicals, instruments, statistical analysis and methodologies which are reported in the publications which might be used in connection with the invention. All references cited in this specification are to be taken as indicative of the level of skill in the art. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

II. DEFINITIONS

“VeA”, as used herein, refers to the amino acid sequences of the VeA protein obtained from Aspergillus nidulans. In addition, VeA shall also refer to the amino acid sequences of VeA obtained from any species (i.e., orthologs), particularly fungi (e.g. other strains and/or species of Aspergillus, and other genera), from any source whether natural, synthetic, semi-synthetic, or recombinant. The term encompasses proteins encoded by nucleotide sequences representing allelic variants as well as those containing single nucleotide polymorphisms (SNPs).

“veA”, as used herein, refers to the nucleotide sequences of the veA gene obtained from Aspergillus nidulans. In addition, veA shall also refer to the nucleotide sequences of the veA gene obtained from any species, particularly fungi (e.g. other strains and/or species of Aspergillus, and other genera), from any source whether natural, synthetic, semi-synthetic, or recombinant. The term encompasses allelic variants and single nucleotide polymorphisms (SNPs).

An “allele” or “allelic sequence”, as used herein, is an alternative form of the gene encoding VeA. Alleles may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or polypeptides whose structure or function may or may not be altered. Any given natural or recombinant gene may have none, one, or many allelic forms. Common mutational changes which give rise to alleles are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.

“Altered” nucleic acid sequences encoding VeA, as used herein, include those with deletions, insertions, or substitutions of different nucleotides resulting in a polynucleotide that encodes the same or a functionally equivalent protein to VeA. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding VeA, and improper or unexpected hybridization to alleles, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding VeA. The encoded protein may also be “altered” and contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent VeA. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues as long as the biological or immunological activity of VeA is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid; positively charged amino acids may include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values may include leucine, isoleucine, and valine, glycine and alanine, asparagine and glutamine, serine and threonine, and phenylalanine and tyrosine.

“Amino acid sequence”, as used herein, refers to an oligopeptide, peptide, polypeptide, or protein sequence, and fragment thereof. Where “amino acid sequence” is recited herein to refer to a particular amino acid sequence “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete amino acid sequence referenced but shall be understood to include fragments of the complete amino acid sequence. The term shall further encompass synthetic molecules as well as those occurring naturally. The term “portion” or “fragment”, as used herein, with regard to an amino acid sequence (as in “a fragment of SEQ ID NO:1”), specifically refers to segments of that amino acid sequence which are not naturally occurring as fragments and would not be found in the natural state. The segments may range in size from five amino acid residues to the entire amino acid sequence minus one amino acid. Thus, a polypeptide “comprising at least a portion of the amino acid sequence of SEQ ID NO:1” or “including an amino acid sequence as set forth in SEQ ID NO:1 or fragments thereof” encompasses the full-length VeA amino acid sequences and segments thereof.

“Amplification”, as used herein, refers to the production of additional copies of a nucleic acid sequence and is generally carried out using polymerase chain reaction (PCR) technologies well known in the art (Dieffenbach, C. W. and G. S. Dveksler (1995) PCR Primer, a Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y.).

“Antisense”, as used herein, refers to any composition containing nucleotide sequences which are complementary to a specific DNA or RNA sequence. The term “antisense strand” is used in reference to a nucleic acid strand that is complementary to the “sense” strand. Antisense molecules include peptide nucleic acids and may be produced by any method including synthesis or transcription. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form duplexes and block either transcription or translation. The designation “negative” is sometimes used in reference to the antisense strand, and “positive” is sometimes used in reference to the sense strand.

“Biologically active”, as used herein, refers to a protein, polypeptide, amino acid sequence, or nucleotide sequence encoding a product having structural, regulatory, or biochemical functions of a naturally occurring molecule. Preferably, a biologically active fragment of VeA will have the secondary metabolite gene cluster regulatory capabilities of a naturally occurring VeA molecule disclosed herein.

“Complementary” or “complementarity”, as used herein, refer to the natural binding of polynucleotides under permissive salt and temperature conditions by base-pairing. For example, the sequence “A-G-T” binds to the complementary sequence “T-C-A”. Complementary between two single-stranded molecules may be “partial”, in which only some of the nucleic acids bind, or it may be complete when total complementarity exists between the single stranded molecules. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, which depend upon binding between nucleic acids strands and in the design and use of PNA molecules.

A “composition comprising a given polynucleotide sequence”, as used herein, refers broadly to any composition containing the given polynucleotide sequence. Compositions comprising polynucleotide sequences encoding VeA or fragments thereof, may be employed as hybridization probes. The probes may be stored in freeze-dried form and may be associated with a stabilizing agent such as a carbohydrate. In hybridizations, the probe may be deployed in an aqueous solution containing salts (e.g., NaCl), detergents (e.g., SDS) and other components (e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.).

The phrase “correlates with expression of a polynucleotide”, as used herein, indicates that the detection of the presence of ribonucleic acid that is similar to SEQ ID NO:1 by northern analysis or equivalent analysis is indicative of the presence of mRNA encoding VeA in a sample and thereby correlates with expression of the transcript from the polynucleotide encoding the protein.

“Deletion”, as used herein, refers to a change in the amino acid or nucleotide sequence and results in the absence of one or more amino acid residues or nucleotides.

“Derivative”, as used herein, refers to the chemical modification of a nucleic acid encoding or complementary to veA or the encoded VeA protein itself. Such modifications include, for example, replacement of hydrogen by an alkyl, acyl, or amino group. A nucleic acid derivative encodes a polypeptide which retains the biological or immunological function of the natural molecule. A derivative polypeptide is one which is modified by glycosylation, or any similar process which retains the biological function of the polypeptide from which it was derived.

“Homology”, as used herein, refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology may be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. A partially complementary sequence that at least partially inhibits an identical sequence from hybridizing to a target nucleic acid is referred to using the functional term “substantially homologous.” The inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (i.e., Southern or northern blot, solution hybridization and the like) under conditions of low stringency. A substantially homologous sequence or hybridization probe will compete for and inhibit the binding of a completely homologous sequence to the target sequence under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction. The absence of non-specific binding may be tested by the use of a second target sequence which lacks even a partial degree of complementary (e.g., less than about 30% identity). In the absence of non-specific binding, the probe will not hybridize to the second non-complementary target sequence.

“Identity”, as used herein, means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Substantial sequence identity” as used herein means at least 80% identical, more preferably 95%, 96%, 97%, 98% or 99% identical. “Identity” and “homology” can be readily calculated by known methods, including but not limited to those described in (Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; and Carillo, H., and Lipman, D., SIAM J. Applied Math., 48: 1073 (1988). Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity and homology are codified in publicly available computer programs. Preferred computer program methods to determine identity and homology between two sequences include, but are not limited to, the GCG program package (Devereux, J., et al., Nucleic Acids Research 12(1): 387 (1984)), BLASTP, BLASTN, and FASTA (Atschul, S. F. et al., J. Molec. Biol. 215: 403-410 (1990). The BLAST X program is publicly available from NCBI and other sources (BLAST Manual, Altschul, S., et al, NCBI NLM NIH Bethesda, Md. 20894; Altschul, S., et al., J. Mol. Biol. 215: 403-410 (1990). The well known Smith Waterman algorithm may also be used to determine identity.

“Hybridization”, as used herein, refers to any process by which a strand of nucleic acid binds with a complementary strand through base pairing.

“Hybridization complex”, as used herein, refers to a complex formed between two nucleic acid sequences by virtue of the formation of hydrogen bonds between complementary G and C bases and between complementary A and T bases; these hydrogen bonds may be further stabilized by base stacking interactions. The two complementary nucleic acid sequences hydrogen bond in an antiparallel configuration. A hybridization complex may be formed in solution (e.g., Co t or Ro t analysis) or between one nucleic acid sequence present in solution and another nucleic acid sequence immobilized on a solid support (e.g., paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells or their nucleic acids have been fixed).

An “insertion” or “addition”, as used herein, refers to a change in an amino acid or nucleotide sequence resulting in the addition of one or more amino acid residues or nucleotides, respectively, as compared to the naturally occurring molecule.

“Isolated” or “purified” or “isolated and purified” means altered “by the hand of man” from its natural state, i.e., if it occurs in nature, it has been changed or removed from its original environment, or both. For example, a polynucleotide or a polypeptide naturally present in a living organism is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is employed herein. Moreover, a polynucleotide or polypeptide that is introduced into an organism by transformation, genetic manipulation or by any other recombinant method is “isolated” even if it is still present in said organism, which organism may be living or non-living. As so defined, “isolated nucleic acid” or “isolated polynucleotide” includes nucleic acids integrated into a host cell chromosome at a heterologous site, recombinant fusions of a native fragment to a heterologous sequence, recombinant vectors present as episomes or as integrated into a host cell chromosome. As used herein, the term “substantially purified”, refers to nucleic or amino acid sequences that are removed from their natural environment, isolated or separated, and are at least 60% free, preferably 75% free, and most preferably 90% free from other components with which they are naturally associated. As used herein, an isolated nucleic acid “encodes” a reference polypeptide when at least a portion of the nucleic acid, or its complement, can be directly translated to provide the amino acid sequence of the reference polypeptide, or when the isolated nucleic acid can be used, alone or as part of an expression vector, to express the reference polypeptide in vitro, in a prokaryotic host cell, or in a eukaryotic host cell.

“Exon”, as used herein, refers to a nucleic acid sequence found in genomic DNA that is bioinformatically predicted and/or experimentally confirmed to contribute contiguous sequence to a mature mRNA transcript.

“Open reading frame” and the equivalent acronym “ORF”, as used herein, refer to that portion of a transcript-derived nucleic acid that can be translated in its entirety into a sequence of contiguous amino acids. As so defined, an ORF has length, measured in nucleotides, exactly divisible by 3. As so defined, an ORF need not encode the entirety of a natural protein.

“Microarray” refers to an ordered arrangement of hybridizable array elements. The array elements are arranged so that there are preferably at least one or more different array elements, more preferably at least 100 array elements, and most preferably at least 1,000 array elements, on a 1 cm² substrate surface. The maximum number of array elements is unlimited, but is at least 100,000 array elements. Furthermore, the hybridization signal from each of the array elements is individually distinguishable. In a preferred embodiment, the array elements comprise polynucleotide representative of fungal-derived polynucleotide sequences.

“Modulate”, as used herein, refers to a change in the activity of VeA. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional or immunological properties of VeA.

“Nucleic acid sequence” or “nucleotide sequence” or “polynucleotide sequence”, as used herein, refers to an oligonucleotide, nucleotide, or polynucleotide, and fragments thereof, and to DNA or RNA of genomic or synthetic origin which may be single- or double-stranded, and represent the sense or antisense strand. Where “nucleic acid sequence” or “nucleotide sequence” or polynucleotide sequence” is recited herein to refer to a particular nucleotide sequence (e.g., the nucleotide sequence set forth in SEQ ID NO:2), “nucleotide sequence”, and like terms, are not meant to limit the nucleotide sequence to the complete nucleotide sequence referenced but shall be understood to include fragments of the complete nucleotide sequence.

In this context, the term “fragment” may be used to specifically refer to those nucleic acid sequences which are not naturally occurring as fragments and would not be found in the natural state. Generally, such fragments are equal to or greater than 15 nucleotides in length, and most preferably includes fragments that are at least 60 nucleotides in length. Such fragments find utility as, for example, probes useful in the detection of nucleotide sequences encoding VeA.

“Sample”, as used herein, is used in its broadest sense. A biological sample suspected of containing nucleic acid encoding VeA, or fragments thereof, or VeA itself may comprise a bodily fluid, extract from a cell, chromosome, organelle, or membrane isolated from a cell, a cell, genomic DNA, RNA, or cDNA (in solution or bound to a solid support, a tissue, a tissue print, and the like).

A “substitution”, as used herein, refers to the replacement of one or more amino acids or nucleotides by different amino acids or nucleotides, respectively. The term “conservative substitution” is used in reference to proteins or peptides to reflect amino acid substitutions that do not substantially alter the activity (specificity or binding affinity) of the molecule. Typically conservative amino acid substitutions involve substitution one amino acid for another amino acid with similar chemical properties (e.g. charge or hydrophobicity). The following six groups each contain amino acids that are typical conservative substitutions for one another: 1) Alanine (A), Serine (S), Threonine (T); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

“Transformation”, as defined herein, describes a process by which exogenous DNA enters and changes a recipient cell. It may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the type of host cell being transformed and may include, but is not limited to, viral infection, electroporation, heat shock, lipofection, and particle bombardment. Such “transformed” cells include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome. They also include cells which transiently express the inserted DNA or RNA for limited periods of time.

A “variant” of VeA, as used herein, refers to an amino acid sequence that is altered by one or more amino acids. The variant may have “conservative” changes, wherein a substituted amino acid has similar structural or chemical properties, e.g., replacement of leucine with isoleucine. More rarely, a variant may have “nonconservative” changes, e.g., replacement of a glycine with a tryptophan. Analogous minor variations may also include amino acid deletions or insertions, or both. Guidance in determining which amino acid residues may be substituted, inserted, or deleted without abolishing biological or immunological activity may be found using computer programs well known in the art, for example, DNASTAR software.

The terms “polypeptide”, “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. The term also includes variations on the traditional peptide linkage joining the amino acids making up the polypeptide. Where the terms are recited herein to refer to a polypeptide, peptide or protein of a naturally occurring protein molecule, the terms are not meant to limit the polypeptide, peptide or protein to the complete, native amino acid sequence associated with the recited protein molecule but shall be understood to include fragments of the complete polypeptide. The term “portion” or “fragment”, as used herein, with regard to a protein or polypeptide (as in “a fragment of the VeA polypeptide”) refers to segments of that polypeptide which are not naturally occurring as fragments in nature. The segments may range in size from five amino acid residues to the entire amino acid sequence minus one amino acid. Thus, a polypeptide “as set forth in SEQ ID NO:1 or a fragment thereof” encompasses the full-length amino acid sequence set forth in SEQ ID NO:1 as well as segments thereof Fragments of VeA preferably are biologically active as defined herein.

The terms “nucleic acid” or “oligonucleotide” or “polynucleotide” or grammatical equivalents herein refer to at least two nucleotides covalently linked together. A nucleic acid of the present invention is preferably single-stranded or double stranded and will generally contain phosphodiester bonds, although in some cases, as outlined below, nucleic acid analogs are included that may have alternate backbones, comprising, for example, phosphoramide (Beaucage et al. (1993) Tetrahedron 49:1925) and references therein; Letsinger (1970) J. Org. Chem. 35:3800; Sprinzl et al. (1977) Eur. J. Biochem. 81: 579; Letsinger et al. (1986) Nucl. Acids Res. 14: 3487; Sawai et al. (1984) Chem. Lett. 805, Letsinger et al. (1988) J. Am. Chem. Soc. 110: 4470; and Pauwels et al. (1986) Chemica Scripta 26: 1419), phosphorothioate (Mag et al. (1991) Nucleic Acids Res. 19:1437; and U.S. Pat. No. 5,644,048), phosphorodithioate (Briu et al. (1989) J. Am. Chem. Soc. 111 :2321, O-methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press), and peptide nucleic acid backbones and linkages (see Egholm (1992) J. Am. Chem. Soc. 114:1895; Meier et al. (1992) Chem. Int. Ed. Engl. 31: 1008; Nielsen (1993) Nature, 365: 566; Carlsson et al. (1996) Nature 380: 207). Other analog nucleic acids include those with positive backbones (Denpcy et al. (1995) Proc. Natl. Acad. Sci. USA 92: 6097; non-ionic backbones (U.S. Pat. Nos. 5,386,023, 5,637,684, 5,602,240, 5,216,141 and 4,469,863; Angew. (1991) Chem. Intl. Ed. English 30: 423; Letsinger et al. (1988) J. Am. Chem. Soc. 110:4470; Letsinger et al. (1994) Nucleoside & Nucleotide 13:1597; Chapters 2 and 3, ASC Symposium Series 580, “Carbohydrate Modifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook; Mesmaeker et al. (1994), Bioorganic & Medicinal Chem. Lett. 4: 395; Jeffs et al. (1994) J. Biomolecular NMR 34:17; Tetrahedron Lett. 37:743 (1996) and non-ribose backbones, including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, Carbohydrate Modifications in Antisense Research, Ed. Y. S. Sanghui and P. Dan Cook. Nucleic acids containing one or more carbocyclic sugars are also included within the definition of nucleic acids (see Jenkins et al. (1995), Chem. Soc. Rev. pp169-176). Several nucleic acid analogs are described in Rawls, C & E News Jun. 2, 1997 page 35. These modifications of the ribose-phosphate backbone may be done to facilitate the addition of additional moieties such as labels, or to increase the stability and half-life of such molecules in physiological environments. As used herein, oligonucleotide is substantially equivalent to the terms “amplimers”, “primers”, “oligomers”, and “probes”, as commonly defined in the art.

The term “heterologous” as it relates to nucleic acid sequences such as coding sequences and control sequences, denotes sequences that are not normally associated with a region of a recombinant construct, and/or are not normally associated with a particular cell. Thus, a “heterologous” region of a nucleic acid construct is an identifiable segment of nucleic acid within or attached to another nucleic acid molecule that is not found in association with the other molecule in nature. For example, a heterologous region of a construct could include a coding sequence flanked by sequences not found in association with the coding sequence in nature. Another example of a heterologous coding sequence is a construct where the coding sequence itself is not found in nature (e.g., synthetic sequences having codons different from the native gene). Similarly, a host cell transformed with a construct which is not normally present in the host cell would be considered heterologous for purposes of this invention.

A “coding sequence” or a sequence which “encodes” a particular polypeptide (e.g. a methyltransferase, etc.), is a nucleic acid sequence which is ultimately transcribed and/or translated into that polypeptide in vitro and/or in vivo when placed under the control of appropriate regulatory sequences. In certain embodiments, the boundaries of the coding sequence are determined by a start codon at the 5′ (amino) terminus and a translation stop codon at the 3′ (carboxy) terminus. A coding sequence can include, but is not limited to, cDNA from prokaryotic or eukaryotic mRNA, genomic DNA sequences from prokaryotic or eukaryotic DNA, and even synthetic DNA sequences. In preferred embodiments, a transcription termination sequence will usually be located 3′ to the coding sequence.

The term “ortholog” refers to genes or proteins which are homologs via speciation, e.g., closely related and assumed to have common descent based on structural and functional considerations. Orthologous proteins function as recognizably the same activity in different species.

Expression “control sequences” or “regulatory elements” refers collectively to promoter sequences, ribosome binding sites, polyadenylation signals, transcription termination sequences, upstream regulatory domains, enhancers, and the like, which collectively provide for the transcription and translation of a coding sequence in a host cell. Not all of these control sequences need always be present in a recombinant vector so long as the desired gene is capable of being transcribed and translated.

“Recombination” refers to the reassortment of sections of DNA or RNA sequences between two DNA or RNA molecules. “Homologous recombination” occurs between two DNA molecules which hybridize by virtue of homologous or complementary nucleotide sequences present in each DNA molecule.

The terms “stringent conditions” or “hybridization under stringent conditions” refers to conditions under which a probe will hybridize preferentially to its target subsequence, and to a lesser extent to, or not at all to, other sequences. “Stringent hybridization” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and northern hybridizations are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes. Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the Tm for a particular probe.

An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is 50% formamide with 1 mg of heparin at 42° C., with the hybridization being carried out overnight. An example of highly stringent wash conditions is 0.15 M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook et al. (1989) Molecular Cloning—A Laboratory Manual (2nd ed.) Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor Press, NY, for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is lx.SSC at 45° C. for 15 minutes. An example low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15 minutes. In general, a signal to noise ratio of 2× (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleic acids which do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.

“Expression vectors” are defined herein as nucleic acid sequences that are direct the transcription of cloned copies of genes/cDNAs and/or the translation of their mRNAs in an appropriate host. Such vectors can be used to express genes or cDNAs in a variety of hosts such as bacteria, bluegreen algae, plant cells, insect cells and animal cells. Expression vectors include, but are not limited to, cloning vectors, modified cloning vectors, specifically designed plasmids or viruses. Specifically designed vectors allow the shuttling of DNA between hosts, such as bacteria-yeast or bacteria-animal cells. An appropriately constructed expression vector preferably contains: an origin of replication for autonomous replication in a host cell, a selectable marker, optionally one or more restriction enzyme sites, optionally one or more constitutive or inducible promoters. In preferred embodiments, an expression vector is a replicable DNA construct in which a DNA sequence encoding VeA or a fragment thereof is operably linked to suitable control sequences capable of effecting the expression of the products in a suitable host. Control sequences include a transcriptional promoter, an optional operator sequence to control transcription and sequences which control the termination of transcription and translation, and so forth.

A “polymorphism” is a variation in the DNA sequence of some members of a species. A polymorphism is thus said to be “allelic,” in that, due to the existence of the polymorphism, some members of a species may have the unmutated sequence (i.e. the original “allele”) whereas other members may have a mutated sequence (i.e. the variant or mutant “allele”). In the simplest case, only one mutated sequence may exist, and the polymorphism is said to be diallelic. In the case of diallelic diploid organisms, three genotypes are possible. They can be homozygous for one allele, homozygous for the other allele or heterozygous. In the case of diallelic haploid organisms, they can have one allele or the other, thus only two genotypes are possible. The occurrence of alternative mutations can give rise to trialleleic, etc. polymorphisms. An allele may be referred to by the nucleotide(s) that comprise the mutation.

“Single nucleotide polymorphism” or “SNPs are defined by their characteristic attributes. A central attribute of such a polymorphism is that it contains a polymorphic site, “X,” most preferably occupied by a single nucleotide, which is the site of the polymorphism's variation. Methods of identifying SNPs are well known to those of skill in the art (see, e.g., U.S. Pat. No. 5,952,174).

Abbreviations used herein include “aa”, amino acid; “MMG”, minimal media glucose; “MMT”, minimal media threonine; “OE”, over expression; “LB”, Luria-Bertani; “nt”, nucleotide; “ORF”, open reading frame; “PCR”, polymerase chain reaction; “PEG”, polyethyleneglycol; “R”, resistant; “WT”, wild-type; and “TS”, temperature sensitive.

III. THE INVENTION

The present invention provides a novel method for producing secondary metabolites by inducing the over-expression of the fungal gene veA (SEQ ID NO: 116—see FIG. 12). Such methods include steps of: (a) obtaining a cell or an organism capable of biosynthesizing a secondary metabolite; (b) transforming the cell or organism with an nucleic acid encoding a VeA polypeptide capable of regulating biosynthesis of the secondary metabolite; and (c) culturing the transformed cell or organism so that an increase in production of the secondary metabolite occurs in the transformed cell or organism as compared to a non-transformed cell or organism.

In one embodiment of the present invention, methods of increasing the amount of a secondary metabolite as described and claimed herein are practiced in an Aspergillus species such as A. nidulans. A. flavus or A. terreus. Secondary metabolites increased by the methods include but are not limited to lovastatin or penicillin.

The invention also provides methods of decreasing the production of a secondary metabolite in a transformed cell or organism. Such methods include the steps of: (a) obtaining a transformed cell or organism capable of biosynthesizing a secondary metabolite, the transformed cell or organism having a defective veA gene wherein the defective veA gene is no longer biologically active and expression of secondary metabolite gene clusters is reduced; and (b) culturing the transformed cell or organism so that a decrease in production of the secondary metabolite occurs in the transformed cell or organism as compared to a non-transformed cell or organism. Such a gene replacement exercise could be carried out by one of skill in the art using techniques presently known in the field. Such a method would be useful in reducing or eliminating production of toxic secondary metabolites in certain organisms. For example, a non-functional variant of veA would be useful in reducing or eliminating aflatoxin production in an A. parasiticus or A. flavus strain transformed thereby. In addition, veA may be targeted by a therapeutic such that veA's ability to regulate secondary metabolite gene cluster activity is inhibited. This approach would provide a therapeutic compound able to reduce the virulence of cells or organisms, thereby providing a treatment for medical maladies involving fungal infections. Methods of identifying inhibitors of target molecules are well known in the art.

In yet another embodiment, the present invention encompasses methods of producing an isolated secondary metabolite. These methods include steps of: (a) obtaining a cell or an organism capable of biosynthesizing a secondary metabolite; (b) transforming the cell or organism with a nucleic acid encoding a VeA polypeptide capable of regulating biosynthesis of the secondary metabolite; (c) culturing the transformed cell or organism under conditions conducive to increasing production of the secondary metabolite in the transformed cell or organism as compared to a non-transformed cell or organism; and (d) recovering the secondary metabolite from the transformed cell or organism in an isolated form.

The invention also provides methods for identifying yet undiscovered secondary metabolite biosynthesis gene clusters in a variety of fungi based on the nucleic acids and transformed cells disclosed herein. Such methods are preferably carried out in a microarray format. For example, using standard microarray technology now commonly employed in the field, one of skill in the art may construct a microarray containing, for example, nucleic acids representative of the expressed genes of wild-type A. nidulans (see, for example, D. Bowtell and J. Sambrook, DNA Microarrays: A Molecular Cloning Manual (2000) Cold Spring Harbor Laboratory Press and P. Baldi and G. W. Hatfield, DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling (2002) Cambridge University Press describing standard microarray techniques data analyses applicable in the present invention). The entire genome for A. nidulans has been sequenced and the sequence is available in annotated form for public use (see the Whitehead Institute/MIT Center for Genome Research website). Construction of the specific nucleic acids affixed to the array substrate may be based on, for example, an expressed sequence tag database provided by the University of Oklahoma.

Using the microarray and standard hybridization techniques known in the field, the expression levels of genes in wild-type A. nidulans, A. flavus or other wild-type fungus versus a veA deletion mutant may then be compared to identify genes whose expression is reduced or absent in the veA deletion mutant compared to the wild-type line. The artisan may subsequently examine the genomic sequence available of, for example, A. nidulans or A. flavus to identify putative secondary metabolite biosynthesis cluster genes in the immediate vicinity of the relevant gene whose expression is initially identified as affected by the absence of veA expression. As secondary metabolite biosynthesis genes are well known to occur in clustered fashion, as described in a plurality of references cited herein, new putative secondary metabolite gene clusters may be identified by this approach.

Further, genes within a putative gene cluster may subsequently be disrupted and the mutant line's production of secondary metabolite products may then be compared with wild-type production in plus/minus fashion to identify the specific natural product produced by the newly-identified gene cluster. The natural product may then be isolated and characterized using standard techniques described and referenced herein.

The above-described screening strategies may be carried out not only between wild-type and veA deletion mutants but also, and more preferably, between veA overexpression mutants and veA deletion mutants to obtain the greatest contrast in veA-influenced secondary metabolite biosynthesis gene expression. As well, the screening methodology described herein is not limited to any one particular fungus but may be applied to any fungus having a veA ortholog (e.g., Aspergillus other than A. nidulans and A. flavus). For example, the genome for Fusarium graminearum is now available and screens utilizing veA overexpression or disruption strains to identify new F. graminearum secondary metabolite gene clusters may certainly be carried out based on the novel materials and teachings provided herein (also see Whitehead Institute/MIT Center for Genomic Research website).

In another embodiment of the invention, nucleotide sequences or fragments thereof which encode VeA may be used in recombinant DNA molecules to direct expression of VeA, fragments or functional equivalents thereof, in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence may be produced, and these sequences may be used to clone and express VeA.

As will be understood by those of skill in the art, it may be advantageous to produce VeA-encoding nucleotide sequences possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce an RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.

The nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter VeA-encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, and/or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. For example, site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, introduce mutations, and so forth.

In another embodiment of the invention, natural, modified, or recombinant nucleic acid sequences encoding VeA may be ligated to a heterologous sequence to encode a fusion protein. For example, to screen peptide libraries for inhibitors of VeA activity, it may be useful to encode a chimeric VeA protein that can be recognized by a commercially available antibody. A fusion protein may also be engineered to contain a cleavage site located between the VeA encoding sequence and the heterologous protein sequence, so that VeA may be cleaved and purified away from the heterologous moiety.

In another embodiment, sequences encoding VeA may be synthesized, in whole or in part, using chemical methods well known in the art. Alternatively, the protein itself may be produced using chemical methods to synthesize the amino acid sequence of VeA, or a fragment thereof. For example, peptide synthesis can be performed using various solid-phase techniques and automated synthesis may be achieved, for example, using the ABI 431A Peptide Synthesizer (Perkin Elmer).

The newly synthesized peptide may be substantially purified by preparative high performance liquid chromatography. The composition of the synthetic peptides may be confirmed by amino acid analysis or sequencing. Additionally, the amino acid sequence of VeA, or any part thereof, may be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins, or any part thereof, to produce a variant polypeptide.

In order to express a biologically active VeA, the nucleotide sequences encoding VeA or functional equivalents may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding VeA and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination.

A variety of expression vector/host systems may be utilized to contain and express sequences encoding VeA. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems. The invention is not limited by the host cell employed.

The “control elements” or “regulatory sequences” are those non-translated regions of the vector—enhancers, promoters, 5′ and 3′ untranslated regions—which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the BLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (Gibco BRL) and the like may be used. The baculovirus polyhedrin promoter may be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (e.g., heat shock, RUBISCO; and storage protein genes) or from plant viruses (e.g., viral promoters or leader sequences) may be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding VeA, vectors based on SV40 or EBV may be used with an appropriate selectable marker.

The following examples describing materials and methodology are offered for illustrative purposes only, and are not intended to limit the scope of the present invention.

III. EXAMPLES Example 1

In the present invention, tandem affinity purification (TAP) was used to identify VeA-interacting proteins (FIG. 1A and FIG. 2A). Final eluates of dark- and light-grown A. nidulans carrying the functional veA gene tagged at its C terminus by TAP tag (veA::ctap*) were analyzed by mass spectrometry. The velvet-like protein B (VelB) (FIG. 3A, 3B), the regulator LaeA, and the a importin KapA were identified as proteins that interact with VeA in the dark (FIG. 1B and Table 4). (Importin is a type of protein that moves other protein molecules into the nucleus by binding to a specific recognition sequence, called the nuclear localization signal (NLS)).

In the light, tagged VeA protein is hardly expressed (FIG. 2B) and only copurifies with VelB. Reciprocal affinity purifications of tagged VelB and LaeA in the dark confirmed the interaction partners, except for the a importin KapA (FIGS. 2C and D). Only tagged VelB can additionally recruit the regulator of sporogenesis VosA in the dark, which seems to be an alternative binding partner for this protein.

Yeast two-hybrid (Y2H) analysis confirmed the VeA-VelB and VeA-LaeA interactions, where VelB and LaeA do not interact in this assay, suggesting that VeA acts as a bridge between VelB and LaeA (FIG. 1C).

The Y2H VosA-LaeA interaction supports a role of LaeA in development (FIG. 4). The C-terminal part of VeA interacts with LaeA, whereas the N-terminal part of VeA, which includes the nuclear localization signal (NLS), is required for interaction with VelB (FIG. 1C and FIG. 4).

VelB, which is conserved in the fungal kingdom, shares 18% amino acid identity with VeA but has no typical NLS (FIG. 3B). Transcript analysis reveals that Ve1B expression increases like that of VeA at late developmental stages (FIG. 3C). The VeA-LaeA and VeA-VelB interactions were visualized by bimolecular fluorescence complementation (BiFC) in living cells. Distinct fluorescent specks show that the VeA-LaeA interaction occurs in the nucleus, whereas VeA and VelB interact in the cytoplasm and within the nucleus (FIGS. 5A and B).

The physical interaction of VeA with VelB, as well as with LaeA, leads to the novel understanding of the present invention that VeA and VelB are functionally interdependent. Similar to veAD, the velBD mutant (FIG. 6A) no longer displays a light-dependent developmental pattern and is unable to form sexual fruit bodies, even in the dark. Asexual sporulation in velBD is impaired but not as strongly as in a veA deletion strain.

Reintroduction of the velB locus fully rescued all of the defects (FIG. 6A). The veAD/velBD double mutant exhibited a near-identical phenotype to that of the veAD single mutant. Neither VelB overexpression in a veAD background nor VeA overexpression in a velBD background rescued the defects of the individual mutants; likewise, LaeA overexpression could not rescue secondary metabolite defects of veAD (FIG. 7).

Unlike overproduction of VeA, overexpression of VelB in a veA+background does not cause excessive production of cleistothecia, but it induces a twofold increase in asexual sporulation in comparison to the wild type (WT). This suggests that VeA controls the number of sexual structures, whereas VelB has additional developmental functions. Secondary metabolism is impaired in veAD, resulting in a similar brownish pigment as is produced by the velBD strain.

Changes in gene expression and in LaeA activity were monitored in the veAD and velBD strains (FIGS. 5C and D, FIGS. 6B and C, and FIG. 8). ST production is abolished in veAD and laeAD strains. In contrast, reduced and delayed but significant ST production in VelBD suggests residual activity of a VeA/LaeA complex in the dark. VeA is enriched in the nucleus in the dark, whereas VelB was found in both the nucleus and the cytoplasm and is hardly affected by illumination (FIGS. 9A and B).

Because LaeA is constitutively nuclear (FIGS. 9A and B) and the interaction of VeA and LaeA occurs in the nucleus (FIG. 5A), VelB has to enter the nucleus, despite the lack of an obvious NLS to fully control LaeA. Localization of the VelB-sGFP fusion protein (where GFP is green fluorescent protein) in a veAD background is shifted toward the cytoplasm, whereas the presence of VeA increases the nuclear localization of VelB (FIGS. 10A and B).

This suggests that VeA can assist VelB to allow an enhanced transport into the nucleus. The data provided herein suggest that the mechanism underlying the coordinated regulation of sexual development and secondary metabolism in A. nidulans is the interaction between the key developmental regulatory complex VelB/VeA and LaeA.

Accordingly, in the dark the VelB/VeA/LaeA velvet complex interaction controls and presumably supports the epigenetic activity of LaeA, which subsequently controls the expression of secondary metabolite gene clusters. In the light, this interaction is diminished because less VeA protein is present, and the entrance of the bridging factor VeA to the nucleus is decreased.

Because the absence of LaeA has a minor impact on development, VeA and VelB have presumably additional functions in fungal differentiation. This is also supported by the identification of VosA, a recently identified regulator of fungal sporogenesis, as an additional binding partner of VelB (FIGS. 2C and D, and Table 4).

Light triggers asexual development, corresponding to the release of high numbers of asexual spores (conidia) into the environment. These phenotypes correlate with the light-dependent cytoplasmic localization of VeA, the constitutive nuclear function of LaeA, and the partial nuclear localization of VelB, respectively. Under light conditions, when low amounts of VeA and VelB are present in the nucleus, the secondary metabolism regulator LaeA seems to be primarily active in those hyphae that are not exposed to light.

Accordingly, the deletion of laeA results in a loss of mycelial pigmentation at the bottom of the colony. The newly described fungal protein VelB, in conjunction with VeA, connects light-dependent development to LaeA-controlled secondary metabolism in A. nidulans. The inventors herein present evidence that the formation of this complex is the molecular basis that synchronizes developmental and metabolic changes to the disappearance of light.

This trimeric complex is designated the “velvet complex”. The VelB/VeA is part of the epigenetic control of chromatin remodeling by modulating LaeA methyltransferase activity (FIG. 10C), in which VeA is functionally active in the dark, forms a complex with increased amounts of VelB, and enhances the transport of VelB to the nucleus.

Because VeA and VelB are both partially nuclear, even in the light, we presume a certain threshold is probably necessary to initiate sexual development and control LaeA. Fungal morphogenesis and secondary metabolism have traditionally been viewed as separate fields. The VelB/VeA/LaeA velvet complex elucidates the molecular mechanisms underlying the intimate relation between fungal development and secondary metabolism.

Strains, media, and growth conditions. Fungal strains used in this study are listed in Table 1.

TABLE 1 Fungal Strains. Strain Genotype Aspergillus nidulans FGSC4 Glasgow wild-type FGSC26 biA1, veA1 FGSC33 biA1; pyroA4, veA1 DVAR1 pabaA1, yA2; argBΔ::trpC; trpC801; veAΔ::argB AGB154 pabaA1 AGB272 pveA::veA, ptrA; pabaA1, yA2; argBΔ::trpC; trpC801, veAΔ::argB AGB273 pveA::veA::ctap* tag, ptrA; pabaA1, yA2; argBΔ::trpC; trpC801, veAΔ::argB AGB274 pveA::veA::sgfp, ptrA; pgpdA::mrfp::h2A, pgpdA::natR; pabaA1, yA2; argBΔ::trpC; trpC801, veAΔ::argB AGB275 pniiA::velB::sgfp::niiAT, pgpdA::natR; pabaA1, yA2; argBΔ::trpC; trpC801, veAΔ::argB AGB276 pniiA::velB::niiAT, pgpdA::natR; pabaA1, yA2; argBΔ::trpC; trpC801, veAΔ::argB AGB152 pyroA4, pyrG89, veA AGB277 pniiA::velB::sgfp::niiAT, A.f. pyrG; pgpdA::mrfp::h2A, pgpdA::natR; pyroA4, pyrG89 AGB278 pniiA::velB::niiAT, A.f. pyrG; pyroA4, pyrG89 TNO2A3 pyrG89, pyroA4 AGB279 velBΔ::ptrA; pyrG89, pyroA4, argB2; nkuAΔ::argB AGB280 pvelB::velB, pgpdA::natR; velBΔ::ptrA; pyrG89, pyroA4, argB2; nkuAΔ::argB AGB281 pniiA::velB::sgfp::niiAT, A.f. pyrG; velBΔ::ptrA; pyrG89, pyroA4, argB2; nkuAΔ::argB AGB282 pveA::veA::sgfp, pgpdA::natR; velBΔ::ptrA; pyrG89, pyroA4, argB2; nkuAΔ::argB AGB283 pniiA::veA::niiAT, A.f. pyrG; velBΔ::ptrA; pyrG89, pyroA4, argB2; nkuAΔ::argB AGB284 pniiA::velB::niiAT, pgpdA::natR; pabaA1, yA2; argBΔ::trpC; trpC801; veAΔ::argB AGB307 pniiA::nyfp::veA::niiAT- pniaD::cyfp::laeA::niaDT, A.f. pyrG; pgpdA::mrfp::h2A, pgpdA::natR; pyroA4, pyrG89 AGB308 pniiA::laeA::sgfp::niiAT, pgpdA::natR AGB310 pniiA::laeA::sgfp::niiAT, pgpdA::natR; pabaA1, yA2; argBΔ::trpC; trpC801; veAΔ::argB AGB311 pniiA::laeA::sgfp::niiAT, pgpdA::natR; velBΔ::ptrA; pyrG89, pyroA4, argB2; nkuAΔ::argB AGB388 pniiA::nyfp::veA::niiAT- pniaD::cyfp::velB::niaDT, A.f. pyrG; pgpdA::mrfp::h2A, pgpdA::natR; pyroA4, pyrG89 AGB389 velB::ctap*::pgpdA::natR AGB390 laeA::ctap*::pgpdA::natR RNI16.1 pyrG89, pyroA4; nkuAΔ::argB; veA1 TNI7.2 velBΔ:: pyrG; pyrG89, pyroA4; nkuAΔ::argB; veA1 RRAW16 pyrG89, yA2; veA RNI18.2 velBΔ:: pyrG; veA RDIT9.32 wild type RJW41.A laeAΔ::metG; veA RJW106.1 velBΔ::pyrG; laeAΔ::metG, veA RJW108.1 veAΔ::argB; trpC::laeA RJW112.2 veAΔ::argB RJW114.11 vosAΔ::argB; laeAΔ::metG, veA RJW116.2 vosAΔ::argB; veA RJW117.18 veAΔ::argB; laeAΔ::metG Saccharomyces cerevisiae EGY48-p1840 MATa his3 trp1 ura3-52 leu2::3LexAop-LEU2 LexAop- LacZ/URA3

A. nidulans TNO2A3 which displays a veA+phenotype served as wild-type for the velB deletion, AGB152 and DVAR1 were used for overexpression experiments. A velB gene replacement cassette comprising 2 kb of velB upstream and downstream flanking regions and the pyrithiamine resistance gene ptrA as selection marker was created (FIG. 11A) and introduced into the nkuAA background strain TNO2A3. The velB deletion mutant TNI7.2 was generated by transforming RNI16.1 with the velB deletion construct with pyrG+. RNI18.2 (ΔvelB;veA+) was isolated from a meiotic cross between RRAW16 and TNI7.2. velB and laeA loci were TAP tagged in nkuAΔ background strain TNO2A3 by using clonNat resistance.

Correct gene replacement was confirmed by Southern analyses (FIG. 11A-C). AGB389 (veA+, velB::ctap*) and AGB390 (veA+, laeA::ctap*) strains were obtained from a meiotic cross between TNO2A3 and AGB154. E. coli DH5α and MACH-1 (INVITROGEN) were applied for plasmid DNA and were propagated in LB medium (1% tryptone, 0.5% yeast extract, 1% NaCl) supplemented with 100-150 μg·ml⁻¹ ampicillin. The bacterial strain KS272 for recombinogenic engineering was propagated in low-salt (0.5% NaCl) LB medium with 25 μg·ml⁻¹ chloramphenicol. Minimal medium (0.52 g·l⁻¹ KCl, 0.52 g·l⁻¹ MgSO4, 1.52 g·l⁻¹ KH2PO4, 0.1% trace element solution, pH6.5) was used for growth of fungal strains, supplemented with appropriate amounts of 4-aminobenzoic acid (PABA, 1 μg·ml⁻¹), Biotin (0.02 μg·ml⁻¹), Uracil (50 μg·ml⁻¹), Pyridoxine (0.05 μg·ml⁻¹), nourseothricin-dihydrogen sulfate (100-120 μg·ml⁻¹) (clonNAT, WERNER BIOAGENTS), pyrithiamine (TAKARA Bio Inc) (0.1 μg·ml⁻¹); 1% D-glucose was used as the source of carbon together with 10 mM ammonium or nitrate as nitrogen source. For TAP experiments, fungal strains were grown in complete medium (0.5% yeast extract, 1% bacto-peptone, 1% glucose). Sterigmatocystin (ST) production of strains was assayed as described.

Transformation procedures. E. coli and A. nidulans cells were transformed as described.

Plasmid constructions details. The plasmids utilized in this work are listed in Table 2, oligonucleotide sequences are given in Table 3.

TABLE 2 Plasmid Constructs. Plasmid Description & Characteristics pPTRII autonomously replicating Aspergillus plasmid [ptrA, AMA1, bla] pPTRII Cloning vector for the construction of LexA DNA binding domain pGAD424 Cloning vector for the construction of GAL4 activation domain pNJ04 veA ORF in pTLexA pNJ05 veA ORF in pGAD424 pNJ06 veA N-terminal (1-300a.a.) in pGAD424 pNJ07 veA C-terminal (276-stop.) in pGAD424 pNJ08 veA1 ORF in pTLexA pNJ09 veA1 ORF in pGAD424 pNJ10 veA1 N-terminal (1-265a.a.) in pGAD424 pNJ11 vosA ORF in pGAD424 pNJ12 vosaA-F239 (1-239a,a) in pGAD424 pNJ13 vosA C-terminal (211a.a-stop) in pGAD424 pNJ14 laeA ORF in pTLexA pNJ15 laeA-F231 (1-231a.a.) in pTLexA pNJ16 laeA-121R (121a.a.-stop) in pTLexA pNJ17 laeA ORF in pGAD424 pNJ18 laeA-F231 (1-231a.a.) in pGAD424 pNJ19 laeA-121R (121a.a.-stop) in pGAD424 pNJ20 velB ORF in pTLexA pNJ21 velB-F231 (1-231 a.a) in pTLexA pNJ22 velB-142R (142a.a.-stop) in pTLexA pNJ23 velB ORF in pGAD424 pNJ24 velB-F231 (1-231 a.a) in pGAD424 pNJ25 velB-142R (142a.a.-stop) in pGAD424 pNV1 Dominant resistance cloning plasmid pME3024 ptrA cassette with SfiI sites in EcoRV site of pBluescript II KS pME3154 veA C-Terminus::ctap* tag::veA 3′ UTR in pGEM5 pME3155 veA 4.6 kb HindIII genomic fragment in pUC19 pME3156 pveA::veA::ctap* tag in pUC19 pME3157 pveA::veA::ctap* tag, ptrA, in pUC19 pME3158 velB deletion cassette [velB::ptrA] pME3159 5 kb velB genomic locus amplicon in ApaI site of pNV1 pME3160 Expression module niiAt -pniiA|pniaD-niaDt-Af pyrG, bla pME3161 pniiA::veA cDNA in PmeI site of pME3160 pME3162 pniiA::velB cDNA in PmeI site of pME3160 pME3163 pniiA::velB::sgfp in PmeI site of pME3160 pME3164 pniiA::velB cDNA in PmeI site of pME3166 expression module pME3165 pniiA::velB::sgfp in PmeI site of pME3166 expression module pME3166 Expression module 2.6 kb amplicon from pME3160 with primers Sv315/318 in ApaI site of pNV1 pME3167 pveA::veA::sgfp, pgpdA::natR in pUC19 pME3168 pveA::veA::sgfp in pUC19 pME3169 pveA::veA::sgfp, ptrA in pUC19 pME3173 pgpdA::intron::mrfp::h2A cDNA in EcoRV and pgpdA::natR in SmaI of pBluescript II KS pME3178 veA 4.6 kb HindIII genomic fragment in HindIII and ptrA in NotI site of pBluescript II KS pME3188 pniiA::n-eyfp::veA cDNA in PmeI, and pniaD::c-eyfp::laeA cDNA in SwaI site of pME3160 expression module pME3189 pniiA::n-eyfp::veA cDNA in PmeI, and pniaD::c-eyfp::velB cDNA in SwaI site of pME3160 expression module pME3190 pniiA::laeA::sgfp in PmeI site of pME3166 expression module

pBluescript II KS (STRATAGENE) and pUC19 (FERMENTAS) were used as cloning plasmids. The plasmid pME3156 containing veA::ctap* tag fusion was constructed by recombineering an 800 bp Earl fragment comprising a C-terminal fusion of the TAP* tag (FIG. 2A) to the veA coding sequence derived from pME3154 with Nad-linearised pME3155 in E. coli. Recombineering is genetic engineering based on homologous recombination in an E. colihost strain expressing phage-derived proteins. In order to create pME3157, a ptrA pyrithiamine resistance cassette was amplified with oligonucleotides Sv129/130 from pPTRII (TAKARA) and inserted into the SmaI site of pME3156, and the final construct was used in tandem affinity purification experiments.

The veA::sgfp fusion in pME3168 was created by replacing the C-TAP* tag module in pME3154 by an OZG28/29-amplified sgfp fragment digested with NcoI/HindIII. pME3168 was digested with SmaI and a blunt ptrA (Sv129/130) was inserted resulting in pME3169. The Gpd1/Nat2-amplified 1.4 kb pgpdA::natR cassette from pNV1 was cloned into SmaI of pME3168 creating pME3167. To create a velB deletion construct, a 2 kb upstream flanking region was amplified (OZG57/58) and inserted into the EcoRV site of pBluescript KS II (STRATAGENE). The resulting plasmid was then used for insertion of a 2 kb velB downstream flanking region (OZG59/60) into Smal site, which was then digested with SfiI to insert the SfiI-released ptrA marker from pME3024 generating pME3158, from which a 5.9 kb replacement cassette was used for deletion of velB locus.

For complementation, pME3159 was created by cloning a 5 kb velB genomic fragment (OZG99/100) in the Apal site of pNV1. For overexpression and localization experiments, the nitrogen source-dependent expression module of pME3160 was exploited, which contains the A. nidulans niiA/niaD intergenic region flanked by the corresponding termination regions to allow expression of two genes in a bidirectional orientation at the same time. The veA and velB cDNAs were amplified and cloned into the PmeI site of pME3160 yielding pME3161 veA and pME3162 velB overexpression constructs, respectively.

The velB cDNA::sgfp fusion construct was created by fusion PCR with OZG63/116 for velB and OZG115/29 for sgfp. To create a dominant expression module, the expression module (niiAT::pniiA/pniaD::niaDT) of pME3160 was amplified with Sv315/318 and cloned into ApaI-digested flushed pNV1 to yield pME3166. The velB cDNA and velB cDNA::sgfp recombinant DNA fragments were cloned into the PmeI site of pME3166. To obtain the pgpdA::mrfp::h2A construct, the gpdA promoter and intron (Sv337/338), mrfp (Sv339/340), h2A cDNA containing terminator (Sv339/340) were amplified. Final products were fused using the double joint PCR procedure. The pgpdA::mrfp::h2A recombinant fragment was cloned into the EcoRV site of pBluescript KS II followed by pgpdA::natR cassette insertion into the SmaI site yielding pME3173. The n-eyfp::veA and c-eyfp::laeA fusion constructs were cloned into the PmeI and SwaI sites of the pME3160, respectively.

For in vivo interaction analyses, n-eyfp (OZG73/74) and veA cDNA (Sv142/143, same as OZG69/70 without restriction sites) were amplified and fused and combined with c-eyfp (OZG75/76) and laeA cDNA (OZG61/62) in plasmid pME3188 and ceyfp (OZG75/77) with velB cDNA (OZG63/64) in pME3189, respectively. The appropriate neyfp::veA, c-eyfp::laeA or c-eyfp::velB fusion constructs were cloned into the Pmel and Swal sites of pME3160.

For the construction of the laeA::sgfp fusion plasmid (pME3190), laeA cDNA (OZG61/162) and sgfp (OZG29/161) were amplified, fused and inserted into the PmeI site of the pME3166 expression module under the niiA promoter.

For construction of the velB and laeA TAP* tag fragments, velB including 400 bp of the 5′ UTR (OZG210/211) and laeA including 400 bp of the 5′ UTR (OZG201/202), velB 1.6 kbp 3′UTR (OZG211/100) and laeA 1.6 kbp 3′UTR (OZG204/205) were amplified from genomic DNA.

These fragments were fused to the ctap*::natR module by fusion PCR, which creates the 5′UTR::velB::ctap*::natR::3′UTR (OZG223/224) and 5′UTR::laeA::ctap*::natR::3′UTR (OZG221/222) gene replacement fragments, respectively.

To confirm protein-protein interaction by a yeast two-hybrid assay, the ORF, N-terminal and C-terminal regions of each gene product were amplified by PCR (Table 3) from an A. nidulans cDNA library provided by Kwang-Yeop Jahng (Chonbuk University, Jeonju, Korea). The PCR product of each gene was digested with EcoRI and SalI or XhoI and cloned into the pTLexA or pGAD424 vector, respectively.

+0 TABLE 3 Oligonucleotides utilized for plasmid generations. Designation Sequence Feature OZG28 5′-TTT GGC CAT GGG TGG TAG CGG TGG TAT GGT GAG CAA sgfp-GGSGG Spacer GGG CGA GGA GCT G-3′ (SEQ ID NO: 1) (NcoI) OZG29 5′-AAA ATT TAA GCT TCT ACT TGT ACA GTT CGT CCA TGC CGT sgfp 3′end (HindIII) G-3′ (SEQ ID NO: 2) OZG57 5′-ACT CAC GAA TCC ACG GGA TAC AT-3′(SEQ ID NO: 3) velB 5′UTR-A OZG58 5′-GGC CTG AGT GGC CGG GTG GGA TAC GGT CCA TCG AAA-3′ velB 5′UTR-B (sfiI) (SEQ ID NO: 4) OZG59 5′-GGC CAT CTA GGC CGA CCG TAT ATT GTT TCA TAA ATC CTT- velB 3′UTR-A (sfiI) 3′ (SEQ ID NO: 5) OZG60 5′-TAT GAC CGC GTG AGC AAA TAG GAC-3′(SEQ ID NO: 6) velB 3′UTR-B OZG61 5′-ATG TTT GAG ATG GGC CCG GTG GG-3′(SEQ ID NO: 7) laeA start OZG62 5′-TTA TCT TAA TGG TTT CCT AGC CTG GT-3′(SEQ ID NO: 8) laeA stop OZG63 5′-ATG TAC GCT GTT GAG GAT AGG GC-3′(SEQ ID NO: 9) velB start OZG64 5′-TTA GTA TTC GTT ATC CAG ACC ATC G-3′(SEQ ID NO: 10) velB stop OZG68 5′-CTC GAG TTA GTA TTC GTT ATC CAG ACC ATC G-3′(SEQ ID velB start (XhoI) NO: 11) OZG69 5′-CCA TGG ATG GCT ACA CTT GCA GCA CCA CCA-3′(SEQ ID NO: veA start (NcoI) 12) OZG70 5′-CTC GAG TTA ACG CAT GGT GGC AGG CTT TGA GA-3′(SEQ ID veA stop(XhoI) NO: 13) OZG73 5′-ATG GTG AGC AAG GGC GAG GAG-3′(SEQ ID NO: 14) n-eyfp start OZG74 5′-GGT GGT GGT GCT GCA AGT GTA GCC ATC GTG GCG ATG n-eyfp::veA fusion GAG CGC ATG ATA TAG-3′(SEQ ID NO: 15) maker OZG75 5′-ATG GCC GAC AAG CAG AAG AAC-3(SEQ ID NO: 16) c-eyfp start OZG76 5′-ACG AGT TCC CAC CGG GCC CAT CTC AAA CAT GTG GTT CAT c-eyfp::laeA fusion GAC CTT CTG TTT CAG-3′(SEQ ID NO: 17) maker OZG77 5′-GGA ATG CGC CCT ATC CTC AAC AGC GTA CAT GTG GTT CAT c-eyfp velB GAC CTT CTG TTT CAG-3′(SEQ ID NO: 18) OZG98 5′-TTT GAA TTC ATG CAG CAG CCC AAG CGC GCG AGA G-3′(SEQ veA1 start ID NO: 19) OZG99 5′-AAA GGG CCC CGA GAA TGT CCG CCT GAC CCG TGC-3′(SEQ velB complement-A ID NO: 20) (ApaI) OZG100 5′-CCA AGT CTG CCC GAC AAG CTC ACT G-3′(SEQ ID NO: 21) velB complement-B OZG115 5′-CGC CAC AGC GAC GAG GAC GAT GGT CTG GAT AAC GAA velB::sgfp fusion TAC GGT GGT AGC GGT GGT ATG GTG AGC AAG-3′(SEQ ID NO: maker 22) OZG116 5′-GTA TTC GTT ATC CAG ACC ATC GTC-3′(SEQ ID NO: 23) velB nostop codon OZG161 5′-CTG CAC ATA TAC CAG GCT AGG AAA CCA TTA AGA GGT laeA::sgfp fusion GGT AGC GGT GGT ATG GTG AGC-3′(SEQ ID NO: 24) maker OZG162 5′-TCT TAA TGG TTT CCT AGC CTG GTA-3′(SEQ ID NO: 25) laeA nostop codon OZG201 5′-CCT CGC CCT CCT GCA TCA ATA TTC GG-3′(SEQ ID NO: 26) laeA 5′UTR OZG202 5′-GAG ACG GCT ATG AAA TTC TTT TTC CAT CTT CTC TTA CCA laeA ctap* fusion CCG CTA CCA CCT CTT AAT GGT TTC CTA GCC TGG TAT ATG-3′ maker (SEQ ID NO: 27) OZG204 5′-GAG CAG GCG CTC TAC ATG AGC ATG CCC TGC CCC TGA laeA 3′UTR-A GAG CAA AAG GCG ACC ACA TCC AGG-3′(SEQ ID NO: 28) (fusion maker) OZG205 5′-TCG TCA ACC GCC TCA GCT GGA ACC-3′(SEQ ID NO: 29) laeA 3′UTR-B OZG210 5′-CCT CCT CGC CGC CTC TAG TAC CGT C-3′(SEQ ID NO: 30) velB 5′UTR OZG211 5′-GAA ATT CTT TTT CCA TCT TCT CTT ACC ACC GCT ACC ACC velB ctap* fusion GTA TTC GTT ATC CAG ACC ATC GTC C-3′(SEQ ID NO: 31) maker OZG212 5′-CGA GCA GGC GCT CTA CAT GAG CAT GCC CTG CCC CTG velB 3′UTR-A AAG ACC GTA TAT TGT TTC ATA AAT CC-3′(SEQ ID NO: 32) (fusion maker) OZG221 5′-CGG CTG TTT ACA TTG TGT TTT CTG G-3′(SEQ ID NO: 33) laeA-NEST-A for fusion OZG222 5′-CCG TGA AGA ACT TGG CGT TGT AG-3′(SEQ ID NO: 34) laeA-NEST-B for fusion OZG223 5′-GGA CCG TCT AAT TCA ACT CAC AG-3′(SEQ ID NO: 35) velB-NEST-A for fusion OZG224 5′-CTT CCA GCG GTT ATC CTC CGT TG-3′(SEQ ID NO: 36) velB-NEST-A for fusion Sv129 5′-ATC TGA CAG AGC GGC CGC AAT TGA TTA CG-3′(SEQ ID NO: ptrA-A 37) Sv130 5′-ATA TAT GCG GCC GCT CTT GCA TCT TTG TTT-3′(SEQ ID NO: ptrA-B 38) Sv315 5′-GAT ACC AAA CGG AAC TGG CTG TTA TGG-3′(SEQ ID NO: 39) expression module A Sv318 5′-ATC GAC GCA ACC ATC GAA GCA GC-3′(SEQ ID NO: 40) expression module B Sv337 5′-GAT CTT TGC CCG GTG TAT GAA ACC-3′(SEQ ID NO: 41) gpdA promoter A  (−432) Sv338 5′-TCG GAG GAG GCC ATG GTG ATG TCT GCT CAA GC-3′(SEQ ID gpdA promoter B NO: 42) Sv339 5′-GAC ATC ACC ATG GCC TCC TCC GAG GAC GTC ATC-3′(SEQ ID mrfp start NO: 43) Sv340 5′-GGC TCC AGC GCC TGC ACC AGC TCC GGC GCC GGT GGA mrfp stop GTG GCG GC-3′(SEQ ID NO: 44) Sv341 5′-GGA GCT GGT GCA GGC GCT GGA GCC ACT GGC GGC AAA h2A start TCT GGT GG-3′(SEQ ID NO: 45) Sv342 5′-ATC TGG AGG GGA CAG GCA GTT TAT-3′(SEQ ID NO: 46) terminator for h2A GpdA 5′-GGG TTT CGA ACT ACA TCA AGG GTC CAA GAC CGA CAT gpdA promoter CGA GGC TCT GTA CAG TGA CCG GTG-3′(SEQ ID NO: 47) Nat2 5′-AGG GAA TTC TCA GGG GCA GGG CAT GC-3′(SEQ ID NO: 48) natR stop OMN131 5′-GAA GGT CGA TGA TGG TGT GAT G-3′(SEQ ID NO: 49) velB 5′ amplify OMN132 5′-CTA GAG GTA AAG ATC AAG GTA G-3′(SEQ ID NO: 50) velB 3′ amplify OMN133 5′-CTG ATG GCT GAA TGA AGC ACA G-3′(SEQ ID NO: 51) velB 5′ nested OMN134 5′-TGC TTT ACG ACG ATA GCC ATG C-3′(SEQ ID NO: 52) velB 3′ nested OMN135 5′-ggtg aag agc att gtt tga ggca GCG GCC AGT CTT  velB 5′ rev with TAG ACA AAT G-3′(SEQ ID NO: 53) pyrG tail (bold) OMN136 5′-agt gcc tcc tct cag aca gaa ta GGA TAA CGA ATA   velB 3′ for with CTA AAG ACC G-3′(SEQ ID NO: 54) pyrG tail (bold) OMN125 5′-TAT GCA CTG GCA CTC AAG CAA CCG-3′(SEQ ID NO: 55) velB forward primer for probe OMN126 5′-GTG CAT GAC GGT CGT ATC TGG TCC-3′(SEQ ID NO: 56) velB reverse primer for probe OKH181 5′-GGC TGT AGT CGC TTT GTT-3′(SEQ ID NO: 57) veA forward primer for probe OKH182 5′-GCC CAG TGT AAG AAA GGA-3′(SEQ ID NO: 58) veA reverse primer for probe OJA242 5′-GCT GTC GAT CTT TGT ACC CTG-3′(SEQ ID NO: 59) laeA forward primer for probe OJA243 5′-CGT TCC TGG ATG TGG TCG CCT-3′(SEQ ID NO: 60) laeA reverse primer for probe oNK11 5′-ATATAAGCTTAATGGCTACACTTGCAGCACCAC-3′(SEQ ID NO: veA forward for 61) Y2H oNK12 5′-ATATGTCGACTTAACGCATGGTGGCAGGCTTTG-3′(SEQ ID NO: veA reverse for Y2H 62) oNK13 5′-ATATAAGCTTAATGCAGCAGCCCAAGCGCGCGAG-3′(SEQ ID veA1 forward for NO: 63) Y2H oNK14 5′-ATATGAATTCATGAGTGCGGCGAACTATCCAG-3′(SEQ ID NO: vosA forward for 64) Y2H oNK15 5′-ATATGTCGACTCACCGAGGAGTTCCGTTCGCTG-3′(SEQ ID NO: vosA reverse for 65) Y2H oNK32 5′-ATATGAATTCATGTTTGAGATGGGCCCGGTGGGAAC-3′(SEQ ID laeA forward for NO: 66) Y2H oNK33 5′-ATATGTCGACTTATCTTAATGGTTTCCTAGCCTG-3′(SEQ ID laeA reverse for NO:67) Y2H oNK74 5′-ATATAAGCTTATCAACGAGCATCAGCACAAAC-3′(SEQ ID veA C-terminal NO:68) forward for Y2H oNK75 5′-ATATGTCGACTCCATATTCCACTGCCGACGGAC-3′(SEQ ID veA N-terminal NO:69) reverse for Y2H oNK76 5′-ATATGAATTCTCTGATAGGACAGCCATGCAAATC-3′(SEQ ID vosA C-terminal NO:70) forward for Y2H oNK78 5′-ATATGAATTCATGTACGCTGTTGAGGATAG-3′(SEQ ID NO:71) velB forward for Y2H oNK79 5′-ATATGTCGACTTAGTATTCGTTATCCAGACCA-3′(SEQ ID NO:72) velB reverse for Y2H oNK130 5′-ATATGAATTCACGGTAGCGCGGGTATCGGAG-3′(SEQ ID NO:73) laeA-121R forward for Y2H oNK132 5′-ATATGAATTCATGTCTTCATCGTATCCACCAC-3′(SEQ ID NO:74) velB-142R forward for Y2H oNK138 5′-ATATCTCGAGACCAGGCACCGGGACGGAGATG-3′(SEQ ID laeA-F231 reverse NO:75) for Y2H oNK140 5′-ATATCTCGAGAGTAGGAATAGTCCCTACTCGTG-3′(SEQ ID vosA-F239 reverse NO:76) for Y2H oNK141 5′-ATATCTCGAGTCCAGGCCCTGGAGTAACTGGCTG-3′(SEQ ID velB-F231 reverse NO:77) for Y2H jwbvelBF 5′-TTCGCTAGACAGCTCATTCTACG-3′(SEQ ID NO:78) velB forward primer for probe jwbvelBR 5′-TAGTATTCGTTATCCAGACCATCG-3′(SEQ ID NO:79) velB reverse primer for probe jwbvelAF 5′-ATACCTGGATAAACCAAATCGAGC-3′(SEQ ID NO:80) veA forward primer for probe jwbvelAR 5′-AGGTTCATTCGCAGGGCTAGAC-3′(SEQ ID NO:81) veA reverse primer for probe jwblaeAF 5′-ACCACTACAGCTACCACTCTCC-3′(SEQ ID NO:82) laeA forward primer for probe jwblaeAR 5′-TTTCGATGCTCTCTGAGACGGC-3′ (SEQ ID NO: 83) laeA reverse primer for probe

Yeast two-hybrid analysis. pTLex (Cho et al., 2003; kindly provided by Suhn-Kee Chae at Paichai University, Daejeon, Korea) derived bait and pGAD424 (CLONTECH) derived prey constructs were cotransformed into the Saccharomyces cerevisiae reporter strain L40 and transformants were selected on -UTL (-ura, -trp, -leu) containing 2% glucose media. To further confirm the interactions of proteins, several transformants of each combination were tested for their coloration on the medium -UTL containing X-Gal, and the transformants were tested for β-galactosidase activity using the yeast β-galactosidase assay kit (PIERCE).

Recombinant DNA procedures, hybridization techniques and analysis of nucleic acids. For recombinant DNA technology, standard protocols were performed. Taq, Pfu (MBI FERMENTAS) and Platinum Taq DNA polymerase (INVITROGEN) were used in PCR reactions, and cloning steps were confirmed by sequencing. Fungal genomic DNA was prepared from ground mycelia, and Southern blot analyses were conducted as described. Total RNA samples were analyzed by Northern hybridization as described. The STRATAGENE Prime-It II kit was used to radioactively label hybridization probes in the presence of [α-32P]dATP.

To produce autoradiographs, washed membranes were exposed to KODAK X-Omat films. Sequence data were analyzed using the LASERGENE software package from DNASTAR, and alignments were created by the Clustal W method. PEST motifs were analyzed on the web tool and NES patterns were identified on the web tool.

TAP purification. The fungal strains AGB272, AGB273 (veA::ctap*), AGB389 (velB::ctap*) and AGB390 (laeA::ctap*) were grown in liquid culture and transferred onto CMM (minimal medium+0.1% casein hydrolysate) plates, wrapped with parafilm and covered with aluminium foil to induce sexual development or were transferred onto MM and incubated under white fluorescent light without wrapping.

At 48 h post induction of sexual and 24 h post induction of asexual development, the differentiating mycelia were ground in liquid nitrogen to prepare crude extracts in B* buffer (100 mM Tris-HCl pH7.6, 250 mM NaCl, 10% glycerol, 0.05% NP-40, 1 mM EDTA, 2 mM DTT) supplemented with an EDTA-free protease inhibitors mix (ROCHE), phosphatase inhibitors (MERCK) and specified protease inhibitors as recommended in the procedure at the NCRR.

Crude extracts were centrifuged for 20 min at 15000 g and transferred into 50 ml falcon tubes. Protein extracts were incubated for 3 h on a rotator with 300 μl of IgG sepharose 6 Fast Flow (AMERSHAM) at 4° C. After that point, the standard protocol (Step 14) as outlined at the NCRR web site was followed with minor modifications. TEV cleavage was executed under rotation using 350U of AcTEV (INVITROGEN) in the presence of 1 μM E-64 (CALBIOCHEM) protease inhibitor at 4° C. for 5 h; 1 mM PMSF (phenylmethanesulfonylfluoride) was included in the calmoduline binding step on affinity resin (STRATAGENE). The TCA (trichloroacetic acid)-precipitated eluate was loaded onto a 10% polyacrylamide gel and stained with Coomassie Brilliant Blue G (Sigma). Protein bands were cut out and submitted for mass spectrometry.

Immunoblotting. For detection of the VeA::TAP* fusion protein and actin, anti-calmodulin binding peptide antibody (UPSTATE, catalog 07-482) and anti-actin antibody (MP Biomedicals, catalog 69100) were used.

LC-MS/MS Protein Identification. Excised polyacrylamide gel pieces of stained protein bands were digested with trypsin according to Shevchenko et al. Tryptic peptides extracted from each gel slice were injected onto a reversed-phase liquid chromatographic column (Dionex-NAN75-15-03-C18 PM) by using the ultimate HPLC system (Dionex, Amsterdam, Netherlands) to further reduce sample complexity prior to mass analyses with an LCQ DecaXP mass spectrometer (ThermoElectron Corp, San Jose, Calif.) equipped with a nanoelectrospray ion source. Cycles of MS spectra with m/z ratios of peptides and four data-dependent MS2 spectra were recorded by mass spectrometry.

The “peak list” was created with extracts provided by the Xcalibur software package (BioworksBrowser 3.1). The MS2 spectra with a total ion current higher than 10,000 were used to search for matches against a public A. nidulans genome-wide protein sequence database of the BROAD INSTITUTE (9542 sequences, December 2005, plus 180 sequences of the most commonly appearing contaminants, e.g., keratins and proteases, provided with the BioworksBrowser package) using the TurboSEQUEST algorithm of the Bioworks software (Version 3.1, Thermo Electron Corp).

The search parameters included based on the TurboSEQUEST algorithm were: (i) precursor ion mass tolerance less than 1.4 amu, (ii) fragment ion mass tolerance less than 1.0 amu, (iii) up to three missed tryptic cleavages allowed, and (iv) fixed cysteine modification by carboxyamidomethylation (plus 57.05 amu) and variable modification by methionine oxidation (plus 15.99 amu) and phosphorylation of serine, threonine, or thyronine (plus 79.97 amu).

In accordance with the criteria described by Link et al., matched peptide sequences of identified proteins had to pass the following: (i) the cross-correlation scores (Xcorr) of matches must be greater than 2.0, 2.5, and 3.0 for peptide ions of charge state 1, 2, and 3, respectively, (ii) ΔCn values of the best peptide matches must be at least 0.4, and (iii) the primary scores (Sp) must be at least 600.

Protein identification required at least two different peptides matching these criteria. The degree of completeness of the b- and y-ion series for each SEQUEST result was manually checked for every protein identified. Peptides of identified proteins were individually blasted against the NCBI database to ensure their unambiguous assignment to the TurboSEQUEST-specified protein. See also the Multiple Consensus Reports for the detailed TurboSEQUEST identifications in the Table 4. The three top scoring peptides are listed for all identifications.

TABLE 4 Mass Spectrometry Data of Protein Identifications. Delta Peptide Sequence MH+ Charge XCorr Cn Sp RSp Ions AN1052.2 (hypothetical protein similar to velvet 1210.3 121 (121-0-0- A)1¹ 0-0) R.LEVISNPFIVYSAK.K(SEQ ID NO: 84) 1580.85 2 5.27 0.59 1188.8 1 21/26 R.LEVISNPFIVYSAK.K(SEQ ID NO: 85) 1425.59 2 4.52 0.32 1075.5 1 18/24 R.LEVISNPFIVYSAK.K(SEQ ID NO: 86) 2135.24 3 6.84 0.66 2085.3 1 37/72 AN0363.2 (hypothetical protein)² 1508.3 151 (150-1-0- 0-0) K.IGVWFVLQDLSVR.T(SEQ ID NO: 87) 1532.81 2 5.18 0.37 1490.4 1 18/24 K.SVSDLPQSDIAEVINK.G(SEQ ID NO: 88) 1715.88 2 5.35 0.55 803.4 1 24/30 R.IWSLQVVQQPIR.A(SEQ ID NO: 89) 1467.74 2 4.62 0.35 1568.4 1 17/22 AN0807.2 (hypothetical protein)³ 186.2 19 (18-0-2-0- 0) K.EIHAYNILHIYQAR.K(SEQ ID NO: 90) 1741.98 2 4.85 0.61 1789.0 1 20/26 R.YAVAGGPAPWNR.N(SEQ ID NO: 91) 1259.40 2 4.70 0.52 1632.0 1 19/22 R.VSESLIYAPHPTNGR.F(SEQ ID NO: 92) 1641.81 2 4.17 0.57 930.5 1 20/28 AN2142.2(hypothetical protein similar to 660.3 66 (66-0-0-0- AF465210_1 karyopherin alpha)⁴ 0) K.IIQVALDGLENILK.V(SEQ ID NO: 93) 1539.84 2 5.09 0.57 2402.5 1 22/26 K.IQAVIEAGIPR.R(SEQ ID NO: 94) 1167.38 2 3.87 0.44 1618.2 1 18/20 K.TPQPDWNTIAPALPVLAK.L(SEQ ID NO: 95) 1933.24 2 4.40 0.64 942.9 1 19/34 AN0363.2(hypothetical protein)⁵ 220.2 22 (22-0-0- 0-0) K.GTAPILASTFSEPFQVFSAK.K(SEQ ID NO: 96) 2099.37  2 5.28 0.47 1045.5 1 22/38 K.IGVWFVLQDLSVR.T(SEQ ID NO: 97) 1532.81  2 4.30 0.43 1499.0  1 18/24 K.SVSDLPQSDIAEVINK.G(SEQ ID NO: 98) 1715.88  2 5.34 0.48 846.1 1 24/30 AN1052.2 (hypothetical protein similar to velvet 778.4 78 (77-1-0- A)⁶ 0-0) K.DATEGTQPMPSPVPGK.L(SEQ ID NO: 99) 1612.79  2 3.70 0.45 516.1 1 18/30 K.KFPGLTTSTPISR.M(SEQ ID NO: 100) 1405.62  2 2.61 0.53 519.5 1 15/24 K.LMTNQGSPVLTGVPVAGVAYLDKPNR.A 2699.12  2 6.16 0.61 737.2 1 35/100 (SEQ ID NO: 101) AN0807.2(hypothetical protein)⁷ 454.3 46 (45-0-0- 1-0) K.EIHAYNILHIYQAR.K(SEQ ID NO: 102) 1741.97  2 3.01 0.59 960.3 1 17/26 R.IQQLAADVK.S(SEQ ID NO: 103) 986.15 2 3.12 0.33 1015.4  1 15/16 R.YAVAGGPAPWNR.N(SEQ ID NO: 104) 1259.40  2 3.39 0.58 1119.0 1 17/22 AN1959.2(hypothetical protein)⁸ 660.3 66 (66-0-0-0- 0) K.DVDNTDGGFFVWGDLSIK.V(SEQ ID NO: 105) 1986.13  2 4.21 0.56 931.0 1 19/34 R.LKDVDNTDGGFFVWGDLSIK.V(SEQ ID NO: 106) 2227.46  2 4.14 0.56 1200.5  1 21/38 AN0807.2(hypothetical protein)⁹ 220.2 22 (22-0-0- 0-0) K.EIHAYNILHIYQAR.K(SEQ ID NO: 107) 1741.97  2 4.15 0.58 1819.4  1 20/26 R.WYNLAVSESIENLSLAPFSR.V(SEQ ID NO: 108) 2297.55  2 4.30 0.54 1495.0  1 22/38 R.YAVAGGPAPWNR.N(SEQ ID NO: 109) 1259.40  2 3.90 0.54 1681.7 1 20/22 AN0363.2(hypothetical protein)¹⁰ 778.4 78 (77-1-0- 0-0) K.GTAPILASTFSEPFQVFSAK.K(SEQ ID NO: 110) 2099.37  3 5.29 0.56  1021.1 1 30/76 K.SVSDLPQSDIAEVINK.G(SEQ ID NO: 111)  1715.88  2 5.59 0.51 799.5 1 21/30 R.IWSLQVVQQPIR.A(SEQ ID NO: 112) 1467.74  2 4.29 0.45 2227.8  1 18/22 AN1052.2(hypothetical protein similar to velvet 454.3 46 (45-0-0- A)¹¹ 1-0) R.LEVISNPFIVYSAK.K(SEQ ID NO: 113) 1580.85  2 4.44 0.55 1269.4  1 21/26 R.RPDQYAGSDAYANAPERPR.S(SEQ ID NO: 114) 2135.24  3 5.25 0.65 1825.0  1 36/72 R.RPSAVEYGQPIAQPYQR.P(SEQ ID NO: 115)  1961.17 3 3.99 0.56 1044.4  1 29/64 ¹Avg. Mass: 63831.1; pI: 9.43; Coverage (amino acids): 39.4% ²Avg. Mass: 37062.4; pI: 5.97; Coverage (amino acids): 30.4% ³Avg. Mass: 41578.2; pI: 5.93; Coverage (amino acids): 28.6% ⁴Avg. Mass: 60627.4; pI: 5.00; Coverage (amino acids): 11% ⁵Avg. Mass: 37062.4; pI: 5.97; Coverage (amino acids): 33.3% ⁶Avg. Mass: 63831.1; pI: 9.43; Coverage (amino acids): 40.6% ⁷Avg. Mass: 41578.2; pI: 5.93; Coverage (amino acids): 18.0% ⁸Avg. Mass: 49010.4; pI: 8.45; Coverage (amino acids): 31.5% ⁹Avg. Mass: 41578.2; pI: 5.93; Coverage (amino acids): 36.6% ¹⁰Avg. Mass: 37062.4; pI: 5.97; Coverage (amino acids): 32.8% ¹¹Avg. Mass: 63831.1; pI: 9.43; Coverage (amino acids): 38.9%

Fluorescence microscopy. A. nidulans spores (5.5×10⁵) were inoculated either on 18 mm×18 mm cover slips submerged in appropriately supplemented liquid medium or on large glass slides covered with a thin layer of medium and incubated at 30° C. overnight. The effect of illumination on localization of VeA and VelB was investigated by growing selected strains in darkness and light on the agar surface or in the submerged culture. Cover slips were mounted on microscope slides using spore storage solution (0.002% Tween, 0.5% NaCl) and fixed with wax.

Fluorescence photographs were taken with a ZEISS Axiovert S100 microscope supported with a HAMAMATSU OCRA-ER digital camera, using the Openlab™ V5.0.1 software package (IMPROVISION, Coventry, UK). For the quantification of the GFP signals, nuclei were defined as ROIs (Area of interest). Pixel intensity within the defined ROIs were analysed by using Openlab tmV5.0.1 software package (IMPROVISION, Coventry, UK). Nuclei were verified by overlaying the GFP and Ds Red signals. Subcellular distribution was observed with a 100× objective using 495 and 558nm extinction and emission filters. No autofluorescence was observed. All images were taken using the same exposure and microscope settings.

Sterigmatocystin extraction and thin layer chromatography (TLC) analysis. Samples (1.6 cm diameter disc with fungal samples and agar together) were collected after asexual developmental induction. The fungal samples were ground in 3 ml ddH₂O in a homogenizer, and then 3 ml chloroform was added to extract ST from the aqueous phase. About 1.8 ml chloroform containing ST was collected after centrifugation, and air-dried. The dried extracts were resuspended in 50 μl of chloroform, and 10 μl were separated in hexane:ethyl acetate (4:1) or chloroform:acetone (4:1) on TLC plates. ImageQuant TL (Amersham Biosciences Co.) was used for ST densitometry. Data are presented as graphs with bars which stand for mean+/−standard error (FIG. 2D). For statistical analysis, data were analyzed using the JMP software package (version 3.2.6, SAS Institute, Inc, Cary, N.C.).

According to the Tukey-Kramer multiple comparison test at P≦0.05, the three mean values for WT in the dark are significantly different from WT in the light and velBA in the dark after 48 hours (FIG. 5D). The graphs without bars do not produce ST above background noise (indicated by “B”).

Example 2

In this example, the inventors created several A. flavus isogenic mutants differing only in copy number of veA and laeA genes, including ΔveA, ΔlaeA, multicopy laeA (MClaeA), and MCveA strains and a double MC strain (MCveA-laeA). The respective VeA and LaeA mutants exhibited critical differences in cell density responses and invasion of host tissues, despite gross similarities between sclerotial and aflatoxin production.

Considering the interdependence of oxylipin function with VeA coupled with the VeA-LaeA interaction, we postulated that VeA mutants would also be impaired in seed pathogenesis in a manner similar to that of LaeA mutants and, furthermore, that both mutants could be affected in density-dependent development. To explore these hypotheses, we created several A. flavus isogenic mutants differing only in copy number of veA and laeA genes, including ΔveA, ΔlaeA, multicopy laeA (MClaeA), and MCveA strains and a double MC strain (MCveA-laeA). The respective VeA and LaeA mutants exhibited critical differences in cell density responses and invasion of host tissues, despite gross similarities between sclerotial and aflatoxin production.

Fungal strains and growth conditions. The Aspergillus flavus strains used and generated in this example are listed in Table 5. ΔveA (SEQ ID NO: 142); containing 5′ veA flanking region (nucleotides 1-1314 in SEQ ID NO: 142), A. fumigatus pyrG (nucleotides 1315-3264 in SEQ ID NO: 142), and 3′ flanking region of the veA open reading frame (nucleotides 3265-4556 in SEQ ID NO: 142). MCveA (SEQ ID NO: 143) was generated by transformation with pSA3.X, and contained A. flavus veA (nucleotides 1368-3156 in SEQ ID NO: 143):: A. fumigatus pyrG (nucleotides 3700-5681 in SEQ ID NO: 143) in TOPO-TA cloning plasmid (TOPO-TA pCR2.1); A.flavus 5′ (nucleotides 259-1367 in SEQ ID NO: 143) and 3′flank (nucleotides 3157-3674 in SEQ ID NO: 143); nucleotides 258, 3675-3679, 3699, 5682-5686 in SEQ ID NO: 143 are restriction sites (EcoRI or SpeI). ΔlaeA (SEQ ID NO: 144) was generated by transformation with PLRM5, and contained A. fumigatus pyrG (nucleotides 1535-3547 in SEQ ID NO: 144), A. flavus 5′ (nucleotides 46-1531 in SEQ ID NO: 144) and 3′flank (nucleotides 3554-4933 in SEQ ID NO: 144); nucleotides 43-45, 1532-1534, 3548-3553, and 4934 in SEQ ID NO: 144 are restriction sites. MClaeA (SEQ ID NO: 145) was generated by transformation with pLRM11, and contained A. parasiticus niaD (nucleotides 2-5128 in SEQ ID NO: 145):: A. flavus laeA (nucleotides 5134-9452 in SEQ ID NO: 145) in Invitrogen pCR bluntll TOPO plasmid (pLRM9); nucleotides 1, and 5129-5133 in SEQ ID NO: 145 are restriction sites. MCveA-laeA was prepared by co-transformation with pSA2.8 and PLRM11 plasmids using A. flavus laeA (SEQ ID NO: 146).

TABLE 5 Aspergillus flavus strains. Strain Genotype * Source NRRL 3357 Wild type Horowitz Brownet al. 2008. Appl. Environ. Microbiol. 74: 5674-5685. NRRL 3357.5 pyrG⁻ Horowitz Brownet al. 2008. Appl. Environ. Microbiol. 74: 5674-5685. TSA 1.54 pyrG⁻ ΔveAr::AfpyrG This study (ΔveA) TSA 2.46 pyrG⁻ AfpyrG veA This study (MCveA) TJW 71.1 pyrG⁻ ΔlaeA::AfpyrG Kale, et al.. 2008. (ΔlaeA) Fungal Genet. Biol. 45: 1422-1429. TJW 79.13 pyrG⁻ ΔlaeA::AfpyrG Kale, et al.. 2008. (MClaeA) niaD⁻ niaD laeA Fungal Genet. Biol 45: 1422-1429. TSA 2.8 pyrG⁻ AfpyrG Horowitz Brownet al. 2008. (MCveA-laeA) veA niaD laeA Appl. Environ. Microbiol. 74: 5674-5685. * Af, A. fumigatus

All strains were maintained as stocks in glycerol and grown at 29° C. on glucose minimal medium (GMM) (36) amended with appropriate supplements for spore production.

Fusion PCR and vector construction. All primers used in this example are listed in Table 6.

TABLE 6  Primer sequences. Primer Sequence (5′-3′) 5′F veA For ACAACCCTGGACTCTGGAAT  (SEQ ID NO: 118) 5′F veA Rev CGAAGAGGGTGAAGAGCATTGTTTGAGGCAGAGG ACGCGTTGACTGTGATG (SEQ ID NO: 119) 3′F veA For TGACGACAATACCTCCCGACGATACC TGGGTTGATTCCTGCTTTTCCTCC  (SEQ ID NO: 120) 3′F veA Rev TCTCGTTCTCCCATTTACCT  (SEQ ID NO: 121) A. fumigatus   TGCCTCAAACAATGCTCTTC  pyrG For (SEQ ID NO: 122) A. fumigatus   CAAGGTATCGTCGGGAGGT  pyrG Rev (SEQ ID NO: 123) Nested For AATCACGGACCTCGAAGCAG  (SEQ ID NO: 124) Nested Rev GGGGTCTTGATATGGCGAAT  (SEQ ID NO: 125) Int veA For CAACAAGACCGACATCACCTTC  (SEQ ID NO: 126) Int veA Rev CCATTCTTGGGATAGCTGCAAC  (SEQ ID NO: 127) MC veA For CAACGAACTAGTCCGCCTGCCCTTAACCTCCA  (SEQ ID NO: 128) MC veA Rev GCATACACTAGTCTCGCATGCCAGTGGATGGG  (SEQ ID NO: 129) veA-pyrG Rev CATCGGTTGACTACGCTCGCA  (SEQ ID NO: 130) laeA-niaD For GACCTGTGGTGAAACCTGAGG  (SEQ ID NO: 131) veA Northern  CTAGCTGGTCATTATTTGATCTCG  For (SEQ ID NO: 132) veA Northern  GTTGTAGAGTGGACGATCATCATG  Rev (SEQ ID NO: 133) laeA Northern   CCTTGTATGATGTATGTATGATGAGC  For (SEQ ID NO: 134) laeA Northern   GACAGCGAAAGTGAAGAGGACATC  Rev (SEQ ID NO: 135) actin Northern  GAAGCGGTCTGAATCTCCTG  For (SEQ ID NO: 136) actin Nothern   ACAGTCCAAGCGTGGTATCC  Rev (SEQ ID NO: 137) aflR Northern   AGAGTCTTCCTTCAGCCAGGTC  For (SEQ ID NO: 138) aflR Northern  GTGGGGCTTTTCTTCATTCTCG  Rev. (SEQ ID NO: 139) *Bold characters flag restriction enzyme (SpeI) site.

The veA replacement PCR products were constructed using fusion PCR following Szewczyk et al. Starting with wild type A. flavus veA (SEQ ID NO: 141, containing 1314 bp of the 5′ flanking region and 1292 bp of the 3′ flanking region of the veA open reading frame), the 1.3-kb fragments upstream and downstream of the veA coding region were amplified by PCR with primers 5′F veA For and Rev for the upstream fragment and primers 3′F veA For and Rev for the downstream fragment, using NRRL 3357 (prototroph) genomic DNA as a template. Next, a 1.9-kb fragment of the pyrG auxotrophy marker gene was amplified from A. fumigatus AF293 genomic DNA using primers A. fumigatus pyrG For and Rev. These three amplified PCR products were cleaned with a QIAquick gel extraction kit (Qiagen), quantified, and fused using published procedures. The PCR product was amplified with primers Nested For and Rev. All PCR steps were performed using an Expand long template PCR system (Roche Diagnostics GmbH, Mannheim, Germany) according to the manufacturer's instructions.

The final construct was confirmed with endonuclease digestion and PCR using primers Int veA For and Rev for internal veA and primers A. fumigatus pyrG For and Rev for pyrG. The veA complementation vector was constructed in two steps. First, the 1.9-kb A. fumigatus pyrG PCR fragment was amplified and ligated into the pCR2.1-TOPO vector (Invitrogen) to create pSA2.4. Next, a 4.4-kb SpeI fragment containing the A. flavus veA gene was amplified from A. flavus NRRL 3357 genomic DNA with primers MC veA For and Rev and ligated into the SpeI site of pSA2.4 to create the veA complementation vector, pSA3.13. The vector was confirmed by PCR with primers MC veA For and veA pyrG Rev and endonuclease digestion.

Fungal transformation procedure and mutant confirmation. For fungal transformation, protoplasts were produced from freshly germinated conidia of NRRL 3357.5 (pyrG auxotroph) and transformed using a polyethylene glycol method. The final fusion PCR product (5 μg) was used for replacement of veA with pyrG after gel purification using a QIAquick gel extraction kit (Qiagen) to create strain TSA 1.54 (SEQ ID NO: 142; containing 1314 bp of the 5′ veA flanking region, 1950 bp of A. fumigatus pyrG, and 1292 bp of the 3′ flanking region of the veA open reading frame). The veA::pyrG vector, pSA3.13, was used alone or else cotransformed with pLRM11.1, a vector containing both laeA and niaD, to create MC strains with multiple copies of veA alone and MC strains with multiple copies of both veA and laeA (TSA 2.46 and TSA 2.8, respectively, were used for these studies).

Correct transformants were identified by analyzing genomic DNA using PCR screens followed by Southern analyses. Primers Int veA For and Rev, Nested For and Rev (4.3 kb for the wild type and 4.6 kb for transformants), and A. fumigatus pyrG For and Rev were used to identify pyrG replacement of veA. MC transformants were identified by PCR with primers MC veA For and veA pyrG Rev and primers laeA-niaD For and laeA Northern Rev. Southern analysis was performed for each PCR-identified transformant to confirm single gene replacement of veA in TSA 1.54, at least 2 copies of veA in TSA 2.46, and at least 2 copies of veA and laeA in TSA 2.8. Probes were created with primers Nested For and Rev for the veA open reading frame (ORF) and primers laeA Northern For and Rev for the laeA ORF.

Northern analysis. To examine the expression of veA and laeA transcripts, Northern analysis was performed. Fifty-milliliter amounts of liquid GMM were inoculated with 10⁶ spores/ml of appropriate strains and incubated with shaking at 250 rpm at 29° C. under dark conditions. After 48 h, the mycelium was collected and total RNA was extracted by using the Trizol method (Invitrogen). Blots were hybridized with a veA fragment amplified using the primers Northern For and Rev, an laeA fragment amplified using the primers Northern For and Rev, an actin fragment amplified using the primers actin Northern For and Rev, and an aflR fragment amplified using the primers aflR Northern For and Rev from NRRL3357 genomic DNA. Detection of signals was carried out with a Phosphorimager-SI (Molecular Dynamics).

Physiological experiments. Conidial production, sclerotial formation, and colony diameter were measured for fungal strains following the methods of Horowitz Brown et al. Briefly, 8-ml amounts of 1.6% GMM plus 2% sorbitol agar were overlaid with 3-ml amounts of 0.7% agar GMM plus 2% sorbitol agar containing 10², 10⁴, and 10⁶ spores/plate of each A. flavus strain for culture. For conidial counts, three 1.5-cm plugs from each plate were homogenized in 5 ml of 0.01% Tween 80 (vol/vol) water, diluted to 1×, and counted with a hematocytometer. To visualize sclerotium formation, plates were sprayed with 70% ethanol to kill and wash away conidia. The exposed sclerotia were then collected, lyophilized, and weighed (dry weight per plate). Growth diameter was measured following a point inoculation of 5 μl of 10⁶ spores/ml for each strain on 30 ml of 1.6% GMM. Cultures were grown at 29° C. under continuous dark or light conditions for 3 days (conidia production), 7 days (sclerotia formation), and 3 and 6 days (colony diameter). Each treatment was replicated four times.

To assay for growth on different fatty acids, the wild-type, ΔlaeA, and ΔveA strains were examined for growth on (i) 20 mM hexanoic acid (6 C), 6 mM oleic acid (18 C), and 4.9 mM erucic acid (22 C) as the sole carbon source, with the fatty acids substituting for the glucose in GMM, or (ii) GMM supplemented with these same molarities of fatty acids, following the method of Maggio-Hall and Keller. Growth diameter was measured following a point inoculation of 5 μl of 10⁶ spores/ml for each strain on 30 ml of medium. Each treatment was replicated four times. The experiment was repeated twice.

Seed infections. For seed/fungal studies, two cultivars (SunRunner and Flo-Runner) of peanut (Arachis hypogaea) and one (Northup King N33-P3) of non-fungicide treatment maize (Zea mays L.) were used. All the steps were aseptically performed as described by Kale et al. Briefly, mature peanuts (20 peanut cotyledons) and maize (10 seeds) were surface sterilized and inoculated with suspensions of 10⁵ spores/ml of each respective strain, as well as with a water control (mock inoculation). Seeds were placed in 50-ml Falcon tubes containing either sterile water or the spore suspensions and shaken for 30 min in a rotary shaker at 50 rpm, after which they were placed in a high-humidity chamber. Peanut cotyledons were incubated for 3 days for peanut cultivar SunRunner or 5 days for cultivar FloRunnner at 29° C. under dark conditions, and maize kernels for 3 days. All seed experiments were repeated three times.

Histological study. Infected and control peanut cotyledons of cultivar Sun-Runner were collected after 3 days of inoculation and sliced with a razor blade into 2-cm pieces which were immersed in ice-cold fixative FAA (3.7% formaldehyde, 5% acetic acid, 47.5% ethanol in water) in vials with vacuum pressure for 30 min. Tissues were then removed, incubated with fresh FAA overnight, dehydrated through a tert-butanol series following the method of Cseke et al., and embedded in paraffin (Paraplast Plus). Paraffin blocks were sectioned in 10-μm slices, and serial sections were placed on glass slides and incubated at 37° C. at least overnight, until tissues adhered to the slides. Dewaxing of tissues and staining with Gomori methenamine-silver were performed in the University of Wisconsin—Madison School of Veterinary Medicine histology services laboratory. For lipid staining in peanut tissues, Nile red was applied to tissues following the method of Tsitsigiannis et al. A tetramethyl rhodamine 5-isothiocyanate filter in a fluorescent microscope (Olympus BX-60 with 546-nm excitation and 585-nm emission filters) was used to observe Nile red-stained tissues.

Aflatoxin extraction from medium. Eight-milliliter amounts of 1.6% GMM-2% sorbitol agar were overlaid with 3-ml amounts of 0.7% GMM agar plus 2% sorbitol agar containing 10², 10⁴, and 10⁶ spores/plate of each fungal strain. Cultures were grown for 3 days at 29° C. under dark or light conditions. Three 1.5-cm plugs from each plate were homogenized in 3 ml of 0.01% Tween 80 (vol/vol) water and vortexed vigorously for 1 min. One milliliter of chloroform was added, and the sample vortexed and incubated at room temperature for 30 min. The mixture was vortexed again and then centrifuged for 15 min. The lower layer was collected, allowed to dry for 3 days, and then resuspended in 100 μl of chloroform, and 40 μl of the suspension was spotted onto TLC plates (Whatman, Maidstone, England) using a chloroform/acetone (95:5, vol/vol) solvent system. Each treatment was repeated three times.

Aflatoxin extraction from seed. Peanut cotyledons and maize kernels inoculated as described above were collected in 50-ml Falcon tubes with the addition of 5 ml of 0.01% Tween 80 and vortexed vigorously for 1 min. One milliliter was removed from each sample for conidium counting prior to aflatoxin extraction. Five milliliters of acetone was then added to the samples, followed by shaking for 10 min in a rotary shaker at 150 rpm. Samples were allowed to stand for 5 min at room temperature, and then 5 ml of chloroform was added to each sample, followed by shaking for 10 min at 150 rpm. Samples were allowed to stand for an additional 10 min at room temperature, vortexed briefly, and centrifuged for 15 min at 2,000 rpm to collect the organic lower phase. This phase was placed in a new tube and then dried completely for 3 days. Five milliliters of 0.1 M NaCl methanol/water (55:45) and 2.5 ml of hexane were added to each tube, and the mixture vortexed vigorously at high speed for 1 min. Samples were centrifuged at 2,000 rpm for 5 min. The hexane layer was collected, the remaining aqueous phase was washed with 2.5 ml of hexane, and then the collection process repeated as described above. The hexane extracts were combined, allowed to dry, and then resuspended in 500 μl of chloroform, and 10 μl of each extract was separated on a silica gel TLC plate using the chloroform/acetone (95:5 vol/vol) solvent system. Each treatment was repeated three times.

Statistical analysis. Statistical differences were analyzed using the JMP software package, version 3.2.6 (SAS Institute, Inc., Cary, N.C.). Multiple comparisons of results for all strains were calculated for growth diameter, lipase activity, and sporulation on seed. To assess the density-dependent development of each strain, sclerotial and conidial numbers were compared at three population levels. Statistically significant mean values, indicated with different letters in the figures, are significant at P<0.05.

Results. Creation of veA and laeA mutant strains in A. flavus. This study required creating near-isogenic strains varying in the number of laeA and veA alleles in the same A. flavus isolate. As ΔlaeA and MC strains of the genome-sequenced strain A. flavus 3357 already existed, the first goal was to obtain near-isogenic strains of A. flavus 3357 with loss of or overexpression of veA.

The sequence of the A. flavus 3357 veA ortholog was obtained by designing primers from the A. flavus ATCC MYA384 veA gene (GenBank DQ296645, SEQ ID NO: 140). The sequences of the two genes were found to be 99% identical. All primers and probes in this study were designed from this sequence (Table 6). FIG. 13A shows the strategy of replacement of veA with A. fumigatus pyrG. Transformants were first screened for loss of production of sclerotia on GMM plus 2% sorbitol medium, a phenotype associated with the A. flavus ATCC MYA384 ΔveA mutant. Several asclerotial A. flavus 3357 transformants were identified and their DNA extracted and analyzed by PCR and Southern analysis. Seventeen out of 100 transformants were found to contain the 4.6-kb and 4.3-kb fragments expected of KpnI (FIG. 13B) and SapI (data not shown) digests, respectively, as expected for a veA replacement with A. fumigatus pyrG. One of these strains, TSA 1.54, was chosen for further studies (FIG. 13B). A strain with at least two copies of veA was obtained by transforming NRRL 3357.5 with plasmid pSA3.13. Several strains were obtained, as determined by Southern analysis, and one, the MCveA strain TSA 2.46, was chosen for further studies (FIG. 13B). Next, a strain with at least two copies of both veA and laeA was obtained by transforming NRRL 3357.5 with plasmids pSA3.13 and pLRM11.1. One of these transformants, the MCveA-laeA strain TSA2.8, was chosen for further studies (FIG. 13B).

The strains with the six genotypes (the wild type and five mutants) exhibited clear differences in development and morphology, as described below, and additionally, the ΔlaeA strain showed a statistically significant inhibition in growth diameter compared to the growth of most other strains under both light and dark conditions. Conversely, the MClaeA strain's growth diameter was greater than the growth diameters of most other strains in both light and dark regimes (FIG. 14).

veA and laeA affect each other's transcription. Kale et al. recently found that laeA expression negatively affects transcription of veA in A. flavus; this result was replicated in our work (FIG. 15). We also found evidence for veA regulation of laeA expression. Although Northern analysis revealed that the AveA strain did not show an increase of laeA expression, the MCveA strain had decreased laeA expression compared to that of the wild type. The MCveA-laeA strain showed relatively high levels of expression of both veA and laeA but not as high as the individual MC strains. We also examined the expression of the aflatoxin-specific transcription factor aflR in all strains. As expected and as previously described, there was no aflR expression in ΔveA and ΔlaeA strains. Similarly to the MClaeA strain, both the MCveA and MCveA-laeA strain showed higher levels of aflR expression than the wild type with this treatment.

Conidial and sclerotial density-dependent production is affected by VeA and LaeA. A recent study has shown that conidial and sclerotial production is density dependent in A. flavus, for which low cell densities resulted in high sclerotial formation and high cell densities in low sclerotial formation, with an inverse effect on conidial production. This quorum-like signaling system regulating the sclerotial-to-conidial shift was impaired in oxylipin-generating oxygenase mutants. Because VeA has been shown to be important in oxylipin signaling responses and forms a complex with LaeA in the nucleus, we now show that changes in veA and laeA expression could affect the density-dependent sclerotial-to-conidial shift.

The relative abilities of the wild type and the veA and laeA mutants to form sclerotia and conidia were determined by inoculating 10², 10⁴, and 10⁶ conidia onto GMM plus 2% sorbitol plates which were placed in constant dark at 29° C. for 3 (conidia) and 7 (sclerotia) days. Similar to prior results, sclerotial production diminished and conidial production increased in the wild type with increasing cell population levels (FIGS. 16A and B). The veA and laeA null mutants were incapable of producing sclerotia at any population level and yielded relatively constant levels of conidial production regardless of population levels (FIGS. 16A and B).

However, clear differences between effects of loss of or overexpression (MC) of veA compared to the results for cognate laeA mutants emerged in both conidial and sclerotial development. Previous studies have suggested a “balance” in sclerotial and conidial production, i.e., when sclerotial production is low, conidial is high and vice versa. This appeared to hold true for the ΔlaeA strain (no sclerotial production at any cell density and high conidial counts at all densities) but not the ΔveA strain, for which conidial counts were very low at all population levels (FIG. 16A) despite the lack of sclerotial production (FIG. 16B). The MC mutants also showed clear differences in their density-dependent responses. The MCveA strain still exhibited a density-dependent response in sclerotial production with declining numbers in both light and dark regimes at high population levels (FIG. 16B). This was in contrast to the MClaeA strain, which maintained constant sclerotial numbers at all population levels (FIG. 16B). The MCveA-laeA double mutant exhibited an intermediate response. The trend to increased conidial numbers at high population levels was maintained in the MCveA and MCveA-laeA strains but not in the MClaeA strain (FIG. 16A). These results are summarized in Table 7.

TABLE 7 Summary of density-dependnent phenomena in A. flavus mutants, morphological differentiations under indicated conditions. Light- Light - Dark- Dark- Mutation Conidia Sclerotia Conidia Sclerotia None (WT) + + + + ΔveA ± − ± − ΔlaeA − − − − MCveA ± + ± + MClaeA − − − − MCveA-laeA + ± + ± + indicates the presence of density-dependent development. ± indicates an intermediate response. − indicates the absence of density-dependent development

Density-dependent production of aflatoxin is controlled by LaeA. We also examined the strains for possible effects of laeA and veA expression on aflatoxin production at all cell densities, as aflatoxin production in the wild type is highest at low population levels. Regardless of cell densities, the ΔveA and ΔlaeA strains never produced observable aflatoxin under the growth conditions used here, whereas all the MC strains produced aflatoxin in all treatments (FIG. 17). The MCveA strain also showed a density-dependent decrease of aflatoxin with increasing cell population, similar to the wild type, whereas the MClaeA strain did not, and the double mutant showed an intermediate result. Aflatoxin production correlated with sclerotial production.

VeA and LaeA are important factors for seed colonization. Recently, Kale et al. reported that laeA mutants were aberrant in host colonization and aflatoxin production on both peanut and maize seed, but there are no reports for the role of VeA in A. flavus pathogenicity. Here, we examined and contrasted colonization attributes of the different veA and laeA mutants on two peanut cultivars and one maize hybrid.

Each fungal strain maintained similar growth patterns regardless of the host seed. FIG. 18A shows that both null mutants produced fewer conidia than the wild type during growth on seeds, with the ΔveA strain developing significantly fewer conidia than the ΔlaeA strain. Visually, the ΔveA strain was most crippled in its ability to grow on any seed (data not shown). The MCveA and MCveA-laeA strains also produced fewer conidia than the wild type; however, the MClaeA strain was similar to the wild type in conidial production, depending on the host seed, as reported earlier. The MC strains also formed sclerotia on the seeds (data not shown).

The colonized seeds were next examined for aflatoxin contamination. All MC strains and the wild type produced aflatoxin in all hosts, in contrast to the lack of aflatoxin production by both the ΔveA and ΔlaeA strain (FIG. 18B). The considerably higher aflatoxin production by some MC mutants in vitro (FIG. 17), however, was not replicated in growth on seed under the conditions in this study.

To further investigate the ability of the strains to colonize seed, histological studies were performed. We were specifically interested in assaying for maceration effects and reasoned that this could be partially measured by host cell lipid utilization. The staining techniques did not show any obvious difference in host penetration by MC strains compared to that of the wild type (data not shown). However, the two null mutants exhibited different host invasion patterns. The results in FIGS. 19A and B show that wild-type hyphae penetrated several layers of host epidermal and mesophyll cells, with accompanying dissolution of host lipid reserves. Although the ΔlaeA strain also penetrated the host cells intracellularly, host lipid reserves were largely intact and the cell integrity appeared less damaged (FIGS. 19A and B). In contrast, hyphae of the ΔveA strain grew intercellularly in epidermal cells and did not appear to penetrate peanut cells as well as hyphae of other strains (FIG. 19A). This mutant, like the ΔlaeA mutant, was also less able to degrade host cell lipid reserves than the wild type (FIG. 19B). However, an in vitro assay for general lipase activity revealed no significant difference between these strains (data not shown).

The wild type and the ΔlaeA and ΔveA strains were then grown on media amended with different fatty acids either as sole carbon source or supplemented with glucose to determine if there might be any gross difference in the ability to utilize or be inhibited by short-, medium-, or long-chain fatty acids. The results did not support any critical difference between the wild type and the two mutants when grown on a fatty acid as the sole carbon source, but the two mutants showed significant inhibition of growth compared to that of the wild type when cultured on GMM amended with oleic acid (FIG. 20). This experiment was repeated twice with similar results (data not shown).

Discussion. In this study, we characterized the function and crossregulation of VeA and LaeA in A. flavus development and pathogenesis. The results, while confirming that VeA and LaeA share functions in regulating aflatoxin and sclerotial production, also demonstrate distinct roles of VeA and LaeA in terms of vegetative growth, conidiation, density-dependent responses, and pattern of colonization of host tissues.

A requirement for LaeA in density-dependent sensing. Quorum-sensing systems in bacteria contribute to the production of virulence factors and biofilm formation in interactions between bacteria and host. In fungi, a quorum-sensing system governing morphological shifts and virulence has been uncovered in the human pathogen Candida albicans. Recently, oxylipin-deficient lipoxygenase and dioxygenase mutants have been found to affect a newly discovered quorum-sensing-like, density-dependent sclerotial-to-conidial morphology shift in A. flavus. Because oxylipin signaling is dependent on VeA function and VeA is part of a nuclear complex with LaeA, we asked if VeA or LaeA mutants could be affected in this quorum-like morphology shift in A. flavus. Both null mutants were blocked in sclerotial formation regardless of cell population, and perhaps due to an inability to produce sclerotia, conidial production was relatively stable for each mutant at all three population levels, although it was much higher in the ΔlaeA strain.

The MC strains showed clear differences in density-dependent development in that an extra copy of LaeA but not VeA abolished this quorum-like phenomenon (FIGS. 16A and B). To date, there are no chemical data identifying molecules regulating the sclerotial-to-conidial switch in A. flavus, although oxylipins are hypothesized to fulfill this function at least in part. Quorum-sensing molecules for Candida albicans (farnesol and tyrosol) and Saccharomyces cerevisiae (phenylethanol and tryptophol) are aromatic alcohols and control the morphological switch from the yeast to filamentous growth in these fungi.

Interestingly, the yeast-to-filamentous growth switch in the fungus Ceratocystis ulmi is attenuated by lipoxygenase inhibitors and may implicate oxylipins in quorum sensing in this tree pathogen. We speculate that A. flavus MClaeA mutants are aberrant in oxylipin production and/or sensing but that this can be remediated to some degree when VeA levels also increase, as demonstrated by the intermediate density-dependent phenotype of the MCveA-laeA strain. The effects of gene loss and gain on density-dependent development are summarized in Table 7.

VeA and LaeA feedback regulation. Both veA and laeA have been reported to be global regulators of secondary metabolites in A. flavus, as well as in other aspergilli. Here, the results indicate that the MCveA and MClaeA strains—particularly the MClaeA strain—produce more aflatoxin and sclerotia than the wild type. The MCveA-laeA double mutant did not show increased toxin production compared to that of the single mutants or an additive effect on sclerotial production. Prior work indicated that LaeA negatively regulated veA expression, and here, we show evidence for VeA regulation of LaeA (FIG. 15), as was described for A. nidulans. These results support a mechanism of mutual repression of veA and laeA expression and may explain, in part, a dampening of the expression of both genes in the MCveA-laeA strain compared to the expression of the single genes in the MCveA and MClaeA strains which, in turn, may affect aflatoxin and sclerotial output in the double mutant.

Requirement for VeA and LaeA in host cell penetration and degradation. Host lipid reserves are depleted during seed colonization by Aspergillus, with lipase and esterase activities implicated in seed pathogenesis. Both null mutants were impaired in seed colonization, where neither strain could degrade lipid reserves despite hyphal penetration of at least some layers of the host seeds (FIGS. 19A and B). The crippled ability of both null mutants to utilize lipid reserves brings to mind several lipid biosynthesis mutants also impaired in Aspergillus colonization of seed, including β-oxidation mutants, odeA mutants [(delta)12-desaturase], and the oxylipin oxygenase mutants in A. nidulans and A. flavus. The inhibition of both null mutants by oleic acid (not seen in the wild type) (FIG. 20) suggests a possible toxic effect of this fatty acid on these strains which may relate to their impairment in growth on seed. It is less likely that the inhibition is associated with defects in β-oxidation, since the mutants grew equally as well as the wild type on oleic acid as a sole carbon source (data not shown), although we cannot rule out this possibility. Regardless of mechanism, the results of all of these studies together may support lipid utilization and/or signaling as an important factor in Aspergillus seed pathogenesis.

Interestingly, the hyphal penetration patterns of the two null mutants as revealed by Gomori staining were quite diverse, whereas hyphae of the ΔveA strain remained largely intercellular (FIG. 19A). This inability to penetrate intracellularly may indicate loss of degradative enzymes in this strain and may explain its poor production of conidia on host seed. However, we note that the strain is crippled in conidial production on medium also. The relative decrease of conidial production by the ΔlaeA strain on seed (compared to its vigorous conidial production in medium) might be attributable to a loss in lipid assimilation or the possible toxicity effects mentioned above.

Histology of the MC strains presented an invasion and lipid degradation pattern similar to that of the wild type. The relatively decreased conidial production on seed from these strains is possibly a function of their skewed sclerotial development rather than an inability to obtain nutrients from the seed.

In conclusion, this example provides additional evidence for distinct roles of LaeA and VeA in the development and pathogenesis of A. flavus despite the considerable overlapping of functions previously reported. The loss of both genes blocks the production of sclerotia and aflatoxin, but under our conditions, only laeA overexpression abolishes density-dependent phenomena, including a sclerotial-to-conidial shift and decreased aflatoxin production with cell population increase. The null mutants, while both were reduced in host lipid utilization, displayed distinct cell ingress abilities as reflected in patterns of hyphal penetration of host cells.

Other embodiments and uses of the invention will be apparent to those skilled in the art from consideration from the specification and practice of the invention disclosed herein. All references cited herein for any reason, including all journal citations and U.S./foreign patents and patent applications, are specifically and entirely incorporated herein by reference. It is understood that the invention is not confined to the specific reagents, formulations, reaction conditions, etc., herein illustrated and described, but embraces such modified forms thereof as come within the scope of the following claims. 

What is claimed is:
 1. A method of increasing the amount of a secondary metabolite produced by a cell or organism comprising the steps of: (a) obtaining a cell or an organism capable of biosynthesizing a secondary metabolite; (b) transforming the cell or organism with a nucleic acid which encodes a veA polypeptide, a polypeptide having substantial sequence identity thereto, or a fragment thereof having secondary metabolite gene cluster regulating activity; and (c) culturing the transformed cell or organism so that an increase in production of the secondary metabolite occurs in the transformed cell or organism as compared to a non-transformed cell or organism.
 2. The method of claim 1 wherein the cell or organism is an Aspergillus species.
 3. The method of claim 2 wherein the Aspergillus species is A. nidulans or A. flavus.
 4. A method of decreasing the production of a secondary metabolite by a transformed cell or organism comprising the steps of: (a) obtaining a transformed cell or organism capable of biosynthesizing a secondary metabolite, the transformed cell or organism having a defective veA gene wherein the defective veA gene is no longer biologically active and expression of secondary metabolite gene clusters is reduced; and (b) culturing the transformed cell or organism so that a decrease in production of the secondary metabolite occurs in the transformed cell or organism as compared to a non-transformed cell or organism.
 5. The method of claim 4 wherein the cell or organism is an Aspergillus species.
 6. The method of claim 5 wherein the Aspergillus species is A. nidulans or A. flavus.
 7. A method of producing an isolated secondary metabolite comprising the steps of: (a) obtaining a cell or an organism capable of biosynthesizing a secondary metabolite; (b) transforming the cell or organism with a nucleic acid which encodes a veA polypeptide, a polypeptide having substantial sequence identity thereto, or a fragment thereof having secondary metabolite gene cluster regulating activity; (c) culturing the transformed cell or organism under conditions conducive to increasing production of the secondary metabolite in the transformed cell or organism as compared to a non-transformed cell or organism; and (d) recovering the secondary metabolite from the transformed cell or organism or from the culture in which the transformed cell or organism was grown in an isolated form.
 8. The method of claim 7 wherein the cell or organism is an Aspergillus species.
 9. The method of claim 8 wherein the Aspergillus species is A. nidulans or A. flavus.
 10. A method for identifying a novel secondary metabolite biosynthesis gene cluster in a fungus comprising steps of: (a) obtaining a transformed fungus having a disrupted veA gene; (b) isolating a sample of nucleic acids from the transformed fungus of step (a), wherein the sample of nucleic acids is representative of the expressed genes of the transformed fungus; (c) hybridizing the sample of nucleic acids isolated in step (b) or nucleic acid equivalents of same with an array comprising a plurality of nucleic acids representative of the expressed genes of a non-transformed fungus under conditions conducive to forming one or more hybridization complexes; (d) detecting the hybridization complexes; (e) comparing the levels of the hybridization complexes detected in step (d) with the level of hybridization complexes detected in a sample of nucleic acids isolated from a veA-expressing fungus, wherein the nucleic acids isolated from a veA-expressing fungus are representative of the expressed genes of the veA-expressing fungus, and wherein an altered level of hybridization complexes detected in step (d) compared with a level of hybridization complexes of the sample of nucleic acids from the veA-expressing fungus correlates with and identifies at least one gene under regulatory control of a veA gene product; and (f) examining genomic nucleotide sequence surrounding the at least one gene identified in step (e) to determine if the at least one gene is clustered with other secondary metabolite biosynthesis genes, thereby identifying a novel secondary metabolite biosynthesis gene cluster.
 11. The method of claim 10 wherein the fungus is an Aspergillus species.
 12. The method of claim 11 wherein the fungus is A. nidulans or A. flavus. 